Citrus Sinensis ID: 023166

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280------
Protein Sequence
MSMSKSSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMTVEGPPPPEESRAKAVSASAVAGPGIGRAAGRGVPAAPLVQAQPGLAGPVRGVGGPAPGMMQPQISRPPIPQLSAPPMTYPATSGGPPVIRPPGQMPPPVYPGQGPPMARGPPPQGPPQGFGVRPPQQFPMPPQQFGQRPMVPPPPGPMMRGPPSGPPRPGMPNAPPPRPGMPPPPGAPVFRPGMPPPPPNAQQQQQNQQQQ
Secondary Structure (PSIPRED)
cccccHHHHHHccccEEEEEEEcccEEEEEEEHHcccccEEEccHHHHHcccccccccccccccccccccccEEEEEcccEEEEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccHHHHHHHcccEEEEEEccccEEEEEEEEEcccccEEEEEEEEEEEEcccccccccEEEEEEEEEEEEEEEEcHHHEEEEEEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHcc
Coil and Loop (DISEMBL)
msmsksskMLQFINYRMRVTIQDGRQLVGKFMAFdrhmnlvlgdceefrklppakgkknntneereDRRTLGLVLLRGEEvismtvegppppeesrakavsasavagpgigraagrgvpaaplvqaqpglagpvrgvggpapgmmqpqisrppipqlsappmtypatsggppvirppgqmpppvypgqgppmargpppqgppqgfgvrppqqfpmppqqfgqrpmvppppgpmmrgppsgpprpgmpnappprpgmppppgapvfrpgmpppppnaqqQQQNQQQQ
Flexible Loop (DISEMBL)
msmsksskMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDceefrklppakgkknntneeredrrtlglvllrgeevismtvegppppEESRAKAVSASAVAGPGIGRAAGRGVPAAPLVQAQPGLAGPVRGVGGPAPGMMQPQISRPPIPQLSAPPMTYPATSGGPPVIRPPGQMPPPVYPGQGPPMARGPPPQGPPQGFGVRPPQQFPMPPQQFGQRPMVPPPPGPMMRGPPSGPPRPGMPNAPPPRPGMPPPPGAPVFRPGMPPPPPNAQQQQQNQQQQ
Low Complexity Region (SEG)
MSMSKSSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMTVEGPPPPEESRakavsasavagpgigraagrgvpaapLVQAQpglagpvrgvggpapgMMQPQISRPPIPQLSAPPMTYPATSGGPPVIRppgqmpppvypgqgppmargpppqgppqgfgvrppqqfpmppqqfgqrpmvppppgpmmrgppsgpprpgmpnappprpgmppppgapvfrpgmpppppnaqqqqqnqqqq
Disordered region (IsUnstruct)
*********LQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEF**********************LGLVLLRGEEV*************************************************************************************************************************************************************************************************************
Disordered Region (DISOPRED)
**********QFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEF*********************TLGLVLLRGEEVISM**********************************************************************************************************************************************************************************************************
Disordered Region (DISEMBL)
********MLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPA*************RRTLGLVLLRGEEVISMT*****************SAVAGPGIGRAAGRGVPAAPLVQAQPGLAGPVRGVGGPAPGMMQPQISRPPIPQLSAPPMTYPATSGGPPVIRPPGQMPPPVYPGQGPPMARGPPPQGPPQGFGVRPPQQFPMPPQQFGQRPMVPPPPGPMMRGPPSGPPRPGMPNAPPPRPGMPPPPGAPVFRPGMPPP**************
Disordered Region (DISPRO)
*****SSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMTVEGPPPPEESRAKAVSAS***********GRGVPAAPLVQAQPGLAGPVRGVGGPAPGMMQPQISRPPIPQLSAPPMTYPATSGGPPVIRPPGQMPPPVYPGQGPPMARGPPPQGPPQGFGVRPPQQFPMPPQQFGQRPMVPPPPGPMMRGPPSGPPRPGMPNAPPPRPGMPPPPGAPVFRPGMPPPPPNAQ*********
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSMSKSSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMTVEGPPPPEESRAKAVSASAVAGPGIGRAAGRGVPAAPLVQAQPGLAGPVRGVGGPAPGMMQPQISRPPIPQLSAPPMTYPATSGGPPVIRPPGQMPPPVYPGQGPPMARGPPPQGPPQGFGVRPPQQFPMPPQQFGQRPMVPPPPGPMMRGPPSGPPRPGMPNAPPPRPGMPPPPGAPVFRPGMPPPPPNAQQQQQNQQQQ
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	286	2.2.26 [Sep-21-2011]
Q9N1Q0	240	Small nuclear ribonucleop	N/A	no	0.503	0.6	0.617	6e-45
Q9PV94	240	Small nuclear ribonucleop	yes	no	0.503	0.6	0.624	2e-37
P14678	240	Small nuclear ribonucleop	yes	no	0.503	0.6	0.617	2e-37
Q9TU67	240	Small nuclear ribonucleop	N/A	no	0.503	0.6	0.617	2e-37
P27048	231	Small nuclear ribonucleop	yes	no	0.503	0.623	0.617	3e-37
Q58DW4	240	Small nuclear ribonucleop	yes	no	0.503	0.6	0.617	3e-37
Q9TU66	240	Small nuclear ribonucleop	no	no	0.503	0.6	0.610	3e-36
Q55A45	274	Small nuclear ribonucleop	yes	no	0.451	0.470	0.571	1e-35
Q05856	199	Small nuclear ribonucleop	yes	no	0.545	0.783	0.537	2e-33
Q10163	147	Small nuclear ribonucleop	yes	no	0.437	0.850	0.489	2e-28

>sp|Q9N1Q0|RSMB_MACEU Small nuclear ribonucleoprotein-associated protein B' OS=Macropus eugenii GN=SNRPB PE=2 SV=1

 Score =  181 bits (458), Expect = 6e-45,   Method: Compositional matrix adjust.
 Identities = 92/149 (61%), Positives = 112/149 (75%), Gaps = 5/149 (3%)

Query: 1   MSMSKSSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNN 60
           M++ KSSKMLQ I+YRMR  +QDGR  +G F AFD+HMNL+L DC+EFRK+ P    KN+
Sbjct: 1   MTVGKSSKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKP----KNS 56

Query: 61  TNEEREDRRTLGLVLLRGEEVISMTVEGPPPPEESRAKAVSASAVAGPGIGRAAGRGVPA 120
              ERE++R LGLVLLRGE ++SMTVEGPPP +   A+   + A  GPGIGRAAGRGVPA
Sbjct: 57  KQAEREEKRVLGLVLLRGENLVSMTVEGPPPKDTGIARVPLSGAAGGPGIGRAAGRGVPA 116

Query: 121 -APLVQAQPGLAGPVRGVGGPAPGMMQPQ 148
             P+ QA  GLAGPVRGVGGP+  +M PQ
Sbjct: 117 GVPMPQAPAGLAGPVRGVGGPSQQVMTPQ 145

Appears to function in the U7 snRNP complex that is involved in histone 3'-end processing. Associated with snRNP U1, U2, U4/U6 and U5. May have a functional role in the pre-mRNA splicing or in snRNP structure. Binds to the downstream cleavage product (DCP) of histone pre-mRNA in a U7 snRNP dependent manner.
Macropus eugenii (taxid: 9315)

>sp|Q9PV94|RSMB_CHICK Small nuclear ribonucleoprotein-associated protein B' OS=Gallus gallus GN=SNRPB PE=2 SV=1

 Score =  156 bits (394), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 93/149 (62%), Positives = 113/149 (75%), Gaps = 5/149 (3%)

Query: 1   MSMSKSSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNN 60
           M++ KSSKMLQ I+YRMR  +QDGR  +G F AFD+HMNL+L DC+EFRK+ P    KN+
Sbjct: 1   MTVGKSSKMLQHIDYRMRCILQDGRVFIGTFKAFDKHMNLILCDCDEFRKIKP----KNS 56

Query: 61  TNEEREDRRTLGLVLLRGEEVISMTVEGPPPPEESRAKAVSASAVAGPGIGRAAGRGVPA 120
              ERE++R LGLVLLRGE ++SMTVEGPPP +   A+   A A  GPG+GRAAGRGVPA
Sbjct: 57  KQPEREEKRVLGLVLLRGENLVSMTVEGPPPKDTGIARVPLAGAAGGPGVGRAAGRGVPA 116

Query: 121 -APLVQAQPGLAGPVRGVGGPAPGMMQPQ 148
            AP+ QA  GLAGPVRGVGGP+  +M PQ
Sbjct: 117 GAPMPQAPAGLAGPVRGVGGPSQQVMTPQ 145

Associated with snRNP U1, U2, U4/U6 and U5. May have a functional role in the pre-mRNA splicing or in snRNP structure.

Gallus gallus (taxid: 9031)

>sp|P14678|RSMB_HUMAN Small nuclear ribonucleoprotein-associated proteins B and B' OS=Homo sapiens GN=SNRPB PE=1 SV=2

 Score =  155 bits (393), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 92/149 (61%), Positives = 112/149 (75%), Gaps = 5/149 (3%)

Query: 1   MSMSKSSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNN 60
           M++ KSSKMLQ I+YRMR  +QDGR  +G F AFD+HMNL+L DC+EFRK+ P    KN+
Sbjct: 1   MTVGKSSKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKP----KNS 56

Query: 61  TNEEREDRRTLGLVLLRGEEVISMTVEGPPPPEESRAKAVSASAVAGPGIGRAAGRGVPA 120
              ERE++R LGLVLLRGE ++SMTVEGPPP +   A+   A A  GPGIGRAAGRG+PA
Sbjct: 57  KQAEREEKRVLGLVLLRGENLVSMTVEGPPPKDTGIARVPLAGAAGGPGIGRAAGRGIPA 116

Query: 121 -APLVQAQPGLAGPVRGVGGPAPGMMQPQ 148
             P+ QA  GLAGPVRGVGGP+  +M PQ
Sbjct: 117 GVPMPQAPAGLAGPVRGVGGPSQQVMTPQ 145

Appears to function in the U7 snRNP complex that is involved in histone 3'-end processing. Associated with snRNP U1, U2, U4/U6 and U5. May have a functional role in the pre-mRNA splicing or in snRNP structure. Binds to the downstream cleavage product (DCP) of histone pre-mRNA in a U7 snRNP dependent manner.

Homo sapiens (taxid: 9606)

>sp|Q9TU67|RSMB_ERIEU Small nuclear ribonucleoprotein-associated protein B' OS=Erinaceus europaeus GN=SNRPB PE=2 SV=1

 Score =  155 bits (393), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 92/149 (61%), Positives = 112/149 (75%), Gaps = 5/149 (3%)

Query: 1   MSMSKSSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNN 60
           M++ KSSKMLQ I+YRMR  +QDGR  +G F AFD+HMNL+L DC+EFRK+ P    KN+
Sbjct: 1   MTVGKSSKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKP----KNS 56

Query: 61  TNEEREDRRTLGLVLLRGEEVISMTVEGPPPPEESRAKAVSASAVAGPGIGRAAGRGVPA 120
              ERE++R LGLVLLRGE ++SMTVEGPPP +   A+   A A  GPGIGRAAGRG+PA
Sbjct: 57  KQAEREEKRVLGLVLLRGENLVSMTVEGPPPKDTGIARVPLAGAAGGPGIGRAAGRGIPA 116

Query: 121 -APLVQAQPGLAGPVRGVGGPAPGMMQPQ 148
             P+ QA  GLAGPVRGVGGP+  +M PQ
Sbjct: 117 GVPMPQAPAGLAGPVRGVGGPSQQVMTPQ 145

Appears to function in the U7 snRNP complex that is involved in histone 3'-end processing. Associated with snRNP U1, U2, U4/U6 and U5. May have a functional role in the pre-mRNA splicing or in snRNP structure. Binds to the downstream cleavage product (DCP) of histone pre-mRNA in a U7 snRNP dependent manner.

Erinaceus europaeus (taxid: 9365)

>sp|P27048|RSMB_MOUSE Small nuclear ribonucleoprotein-associated protein B OS=Mus musculus GN=Snrpb PE=1 SV=1

 Score =  155 bits (393), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 92/149 (61%), Positives = 112/149 (75%), Gaps = 5/149 (3%)

Query: 1   MSMSKSSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNN 60
           M++ KSSKMLQ I+YRMR  +QDGR  +G F AFD+HMNL+L DC+EFRK+ P    KN+
Sbjct: 1   MTVGKSSKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKP----KNS 56

Query: 61  TNEEREDRRTLGLVLLRGEEVISMTVEGPPPPEESRAKAVSASAVAGPGIGRAAGRGVPA 120
              ERE++R LGLVLLRGE ++SMTVEGPPP +   A+   A A  GPGIGRAAGRG+PA
Sbjct: 57  KQAEREEKRVLGLVLLRGENLVSMTVEGPPPKDTGIARVPLAGAAGGPGIGRAAGRGIPA 116

Query: 121 -APLVQAQPGLAGPVRGVGGPAPGMMQPQ 148
             P+ QA  GLAGPVRGVGGP+  +M PQ
Sbjct: 117 GVPMPQAPAGLAGPVRGVGGPSQQVMTPQ 145

Appears to function in the U7 snRNP complex that is involved in histone 3'-end processing (By similarity). Associated with snRNP U1, U2, U4/U6 and U5. May have a functional role in the pre-mRNA splicing or in snRNP structure. Binds to the downstream cleavage product (DCP) of histone pre-mRNA in a U7 snRNP dependent manner.

Mus musculus (taxid: 10090)

>sp|Q58DW4|RSMB_BOVIN Small nuclear ribonucleoprotein-associated protein B' OS=Bos taurus GN=SNRPB PE=2 SV=1

 Score =  155 bits (392), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 92/149 (61%), Positives = 112/149 (75%), Gaps = 5/149 (3%)

Query: 1   MSMSKSSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNN 60
           M++ KSSKMLQ I+YRMR  +QDGR  +G F AFD+HMNL+L DC+EFRK+ P    KN+
Sbjct: 1   MTVGKSSKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKP----KNS 56

Query: 61  TNEEREDRRTLGLVLLRGEEVISMTVEGPPPPEESRAKAVSASAVAGPGIGRAAGRGVPA 120
              ERE++R LGLVLLRGE ++SMTVEGPPP +   A+   A A  GPGIGRAAGRG+PA
Sbjct: 57  KQAEREEKRVLGLVLLRGENLVSMTVEGPPPKDTGIARVPLAGAAGGPGIGRAAGRGIPA 116

Query: 121 -APLVQAQPGLAGPVRGVGGPAPGMMQPQ 148
             P+ QA  GLAGPVRGVGGP+  +M PQ
Sbjct: 117 GVPMPQAPAGLAGPVRGVGGPSQQVMTPQ 145

Appears to function in the U7 snRNP complex that is involved in histone 3'-end processing. Associated with snRNP U1, U2, U4/U6 and U5. May have a functional role in the pre-mRNA splicing or in snRNP structure. Binds to the downstream cleavage product (DCP) of histone pre-mRNA in a U7 snRNP dependent manner.

Bos taurus (taxid: 9913)

>sp|Q9TU66|RSMB_MONDO Small nuclear ribonucleoprotein-associated protein B' OS=Monodelphis domestica GN=SNRPB PE=2 SV=1

 Score =  152 bits (384), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 91/149 (61%), Positives = 111/149 (74%), Gaps = 5/149 (3%)

Query: 1   MSMSKSSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNN 60
           M++ KSSKMLQ I+ RMR  +QDGR  +G F AFD+HMNL+L DC+EFRK+ P    KN+
Sbjct: 1   MTVGKSSKMLQHIDCRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKP----KNS 56

Query: 61  TNEEREDRRTLGLVLLRGEEVISMTVEGPPPPEESRAKAVSASAVAGPGIGRAAGRGVPA 120
              ERE++R LGLVLLRGE ++SMTVEGPPP +   A+   A A  GPGIGRAAGRGVPA
Sbjct: 57  KQAEREEKRVLGLVLLRGENLVSMTVEGPPPKDTGIARVPLAGAAGGPGIGRAAGRGVPA 116

Query: 121 -APLVQAQPGLAGPVRGVGGPAPGMMQPQ 148
             P+ QA  GLAGP+RGVGGP+  +M PQ
Sbjct: 117 GVPMPQAPAGLAGPIRGVGGPSQQVMTPQ 145

Appears to function in the U7 snRNP complex that is involved in histone 3'-end processing. Associated with snRNP U1, U2, U4/U6 and U5. May have a functional role in the pre-mRNA splicing or in snRNP structure. Binds to the downstream cleavage product (DCP) of histone pre-mRNA in a U7 snRNP dependent manner.

Monodelphis domestica (taxid: 13616)

>sp|Q55A45|RSMB_DICDI Small nuclear ribonucleoprotein-associated protein B OS=Dictyostelium discoideum GN=snrpb PE=3 SV=1

 Score =  150 bits (379), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 84/147 (57%), Positives = 103/147 (70%), Gaps = 18/147 (12%)

Query: 5   KSSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEE 64
           KSSKMLQ+INYRMRVTIQDGR +VG+F+AFD+HMN+V+ D EEFR++   KGK     E+
Sbjct: 6   KSSKMLQYINYRMRVTIQDGRVIVGRFLAFDKHMNVVICDAEEFRRIRQ-KGK-----ED 59

Query: 65  REDRRTLGLVLLRGEEVISMTVEGPPPPEESRAKAVSASAV-----AGPGIGRAAGR--- 116
           RE++RTLG++L+RGE V+SM+VE PPP E   AK  + S +      GPGIGRA GR   
Sbjct: 60  REEKRTLGMILIRGETVVSMSVEAPPPEE---AKLAATSKMPPQIPGGPGIGRAVGRGMP 116

Query: 117 -GVPAAPLVQAQPGLAGPVRGVGGPAP 142
            G           GL GPVRGVGGPAP
Sbjct: 117 MGGMGMGGSGPMSGLTGPVRGVGGPAP 143

May have a functional role in the pre-mRNA splicing or in snRNP structure.

Dictyostelium discoideum (taxid: 44689)

>sp|Q05856|RSMB_DROME Small nuclear ribonucleoprotein-associated protein B OS=Drosophila melanogaster GN=SmB PE=1 SV=1

 Score =  143 bits (360), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 87/162 (53%), Positives = 109/162 (67%), Gaps = 6/162 (3%)

Query: 1   MSMSKSSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNN 60
           M++ K++KM+Q +NYR+R+ +QD R  +G F AFD+HMNL+LGDCEEFRK+      KN+
Sbjct: 1   MTIGKNNKMIQHLNYRVRIVLQDSRTFIGTFKAFDKHMNLILGDCEEFRKIR----SKNS 56

Query: 61  TNEEREDRRTLGLVLLRGEEVISMTVEGPPPPEESRAKAVSASAVAGPGIGRAAGRGVPA 120
              ERE++R LG VLLRGE ++S+TVEGPPPPEE   +     A  GPGIGR AGRG+P 
Sbjct: 57  KVPEREEKRVLGFVLLRGENIVSLTVEGPPPPEEGLPRVPIPGAAPGPGIGRVAGRGMPI 116

Query: 121 APLVQAQPGLAGPVRGVGGPAPGMMQPQ-ISRPPIPQLSAPP 161
             L     GL GPVRGVGGPA   M P     P  P + APP
Sbjct: 117 N-LSAVPAGLQGPVRGVGGPAQQHMAPMGRGVPRAPMMGAPP 157

May have a functional role in pre-mRNA splicing or in snRNP structure. Involved in germline establishment and development.

Drosophila melanogaster (taxid: 7227)

>sp|Q10163|RSMB_SCHPO Small nuclear ribonucleoprotein-associated protein B OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=smb1 PE=1 SV=1

 Score =  126 bits (317), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 68/139 (48%), Positives = 95/139 (68%), Gaps = 14/139 (10%)

Query: 6   SSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNN--TNE 63
           ++KM+  +N+ + VT +DGR  VG+ +AFD  MNLVL DC+E+R +     KK N  +N 
Sbjct: 3   TTKMVSLLNHSLNVTTKDGRTFVGQLLAFDGFMNLVLSDCQEYRHI-----KKQNVPSNS 57

Query: 64  EREDRRTLGLVLLRGEEVISMTVEGPPPPEESRAKAVSASAVAGPGIGRAAGRGVPAAPL 123
             E++R LGLV+LRGE ++S++V+GPPP + S    +  S ++GPG+ R AGRG+   PL
Sbjct: 58  VYEEKRMLGLVILRGEFIVSLSVQGPPPMDPS----MRGSLLSGPGVARPAGRGI---PL 110

Query: 124 VQAQPGLAGPVRGVGGPAP 142
            QA  GLAGPVRGVG  AP
Sbjct: 111 GQAPVGLAGPVRGVGYTAP 129

Involved in pre-mRNA splicing. Binds snRNA U1, U2, U4 and U5 which contain a highly conserved structural motif called the Sm binding site.

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	286
255578055	275	small nuclear ribonucleoprotein-associat	0.734	0.763	0.806	7e-85
255578051	275	small nuclear ribonucleoprotein-associat	0.734	0.763	0.801	3e-84
357494377	394	Small nuclear ribonucleoprotein-associat	0.685	0.497	0.808	2e-81
224115254	289	predicted protein [Populus trichocarpa]	0.793	0.785	0.846	7e-81
449433521	284	PREDICTED: small nuclear ribonucleoprote	0.639	0.644	0.879	6e-80
356501499	282	PREDICTED: small nuclear ribonucleoprote	0.618	0.627	0.872	2e-79
225463717	276	PREDICTED: small nuclear ribonucleoprote	0.695	0.721	0.861	4e-79
118482995	286	unknown [Populus trichocarpa]	0.902	0.902	0.816	4e-79
356553373	281	PREDICTED: small nuclear ribonucleoprote	0.618	0.629	0.867	8e-79
224117856	250	predicted protein [Populus trichocarpa]	0.618	0.708	0.892	3e-78

>gi|255578055|ref|XP_002529898.1| small nuclear ribonucleoprotein-associated protein, putative [Ricinus communis] gi|223530625|gb|EEF32501.1| small nuclear ribonucleoprotein-associated protein, putative [Ricinus communis]

 Score =  319 bits (818), Expect = 7e-85,   Method: Compositional matrix adjust.
 Identities = 183/227 (80%), Positives = 188/227 (82%), Gaps = 17/227 (7%)

Query: 1   MSMSKSSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNN 60
           MSMSKSSKMLQ INYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNN
Sbjct: 1   MSMSKSSKMLQHINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNN 60

Query: 61  TNEEREDRRTLGLVLLRGEEVISMTVEGPPPPEESRAKAVSASAVAGPGIGRAAGRGVPA 120
             EEREDRRTLGLVLLRGEEVISMTVEGPPP EESRAKAVSA+AVAGPGIGRAAGRG+P 
Sbjct: 61  --EEREDRRTLGLVLLRGEEVISMTVEGPPPQEESRAKAVSATAVAGPGIGRAAGRGIPT 118

Query: 121 APLVQAQPGLAGPVRGVGGPAPGMMQPQISRPPIPQLSAPPMTYPATSGGPPVIRPPGQM 180
           APL+QAQPGLAGPVRGVGGPAPGMMQPQISRPP+PQLSAPPM+YP     PPVIRPPGQM
Sbjct: 119 APLIQAQPGLAGPVRGVGGPAPGMMQPQISRPPVPQLSAPPMSYP-----PPVIRPPGQM 173

Query: 181 PPPVYPGQGPPMARGPPPQGPPQGFGVRPP---QQFPM-PPQQFGQR 223
                               PP  FG RPP   Q FPM PP QFGQR
Sbjct: 174 ------AFPGQGPPPMGRGPPPPQFGARPPPPGQGFPMPPPPQFGQR 214

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255578051|ref|XP_002529896.1| small nuclear ribonucleoprotein-associated protein, putative [Ricinus communis] gi|223530623|gb|EEF32499.1| small nuclear ribonucleoprotein-associated protein, putative [Ricinus communis]

 Score =  317 bits (813), Expect = 3e-84,   Method: Compositional matrix adjust.
 Identities = 182/227 (80%), Positives = 187/227 (82%), Gaps = 17/227 (7%)

Query: 1   MSMSKSSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNN 60
           MSMSKSSKMLQ INYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNN
Sbjct: 1   MSMSKSSKMLQHINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNN 60

Query: 61  TNEEREDRRTLGLVLLRGEEVISMTVEGPPPPEESRAKAVSASAVAGPGIGRAAGRGVPA 120
             EEREDRRTLGLVLLRGEEVISMTVEGPPP EESRAKAVSA+AVAGPGIGRAAGRG+P 
Sbjct: 61  --EEREDRRTLGLVLLRGEEVISMTVEGPPPQEESRAKAVSATAVAGPGIGRAAGRGIPT 118

Query: 121 APLVQAQPGLAGPVRGVGGPAPGMMQPQISRPPIPQLSAPPMTYPATSGGPPVIRPPGQM 180
           APL+QAQPGLAGPVRGVGGPAPGMMQPQISRPP+PQLSAPPM+YP     PPVIRPPGQM
Sbjct: 119 APLIQAQPGLAGPVRGVGGPAPGMMQPQISRPPVPQLSAPPMSYP-----PPVIRPPGQM 173

Query: 181 PPPVYPGQGPPMARGPPPQGPPQGFGVRPP---QQFPM-PPQQFGQR 223
                               PP  FG RPP   Q FPM PP  FGQR
Sbjct: 174 ------AFPGQGPPPMGRGPPPPQFGARPPPPGQGFPMPPPPHFGQR 214

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357494377|ref|XP_003617477.1| Small nuclear ribonucleoprotein-associated protein B [Medicago truncatula] gi|355518812|gb|AET00436.1| Small nuclear ribonucleoprotein-associated protein B [Medicago truncatula]

 Score =  308 bits (788), Expect = 2e-81,   Method: Compositional matrix adjust.
 Identities = 169/209 (80%), Positives = 184/209 (88%), Gaps = 13/209 (6%)

Query: 1   MSMSKSSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNN 60
           MS+SKSSKMLQ+INYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKK  
Sbjct: 1   MSLSKSSKMLQYINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKT- 59

Query: 61  TNEEREDRRTLGLVLLRGEEVISMTVEGPPPPEESRAKAVSASAVAGPGIGRAAGRGVPA 120
           T+ +REDRRTLGLVLLRGEEVISM VEGPPPPEESR+KAV+A+A+AGPGIGRAAGRG+P 
Sbjct: 60  TDGDREDRRTLGLVLLRGEEVISMAVEGPPPPEESRSKAVNAAAMAGPGIGRAAGRGIPP 119

Query: 121 APLVQAQPGLAGPVRGVGGPAPGMMQPQISRPPIPQLSAPPMTYPATSGGPPVIRPPGQM 180
           AP++QAQPGLAGPVRGVGGPAPGMMQPQISRPP+        +YP   GGPPV+RPPGQM
Sbjct: 120 APVIQAQPGLAGPVRGVGGPAPGMMQPQISRPPV--------SYP---GGPPVMRPPGQM 168

Query: 181 PPPVYPGQGPP-MARGPPPQGPPQGFGVR 208
           P P +PGQGPP M RGPPP  PP  FG R
Sbjct: 169 PYPGHPGQGPPQMVRGPPPPMPPGQFGQR 197

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224115254|ref|XP_002332199.1| predicted protein [Populus trichocarpa] gi|222875306|gb|EEF12437.1| predicted protein [Populus trichocarpa]

 Score =  306 bits (784), Expect = 7e-81,   Method: Compositional matrix adjust.
 Identities = 199/235 (84%), Positives = 209/235 (88%), Gaps = 8/235 (3%)

Query: 1   MSMSKSSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNN 60
           MSMSKSSKMLQ+INYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNN
Sbjct: 1   MSMSKSSKMLQYINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNN 60

Query: 61  TNEEREDRRTLGLVLLRGEEVISMTVEGPPPPEESRAKAVSASAVAGPGIGRAAGRGVPA 120
             EEREDRRTLGLVLLRGEEVISMTVEGPPPPEESRAKAVSA+A +GPG+GRAAGRG+P 
Sbjct: 61  --EEREDRRTLGLVLLRGEEVISMTVEGPPPPEESRAKAVSAAAASGPGLGRAAGRGIPT 118

Query: 121 APLVQAQPGLAGPVRGVGGPAPGMMQPQISRPPIPQLSAPPMTYPATS----GGPPVIRP 176
           APL+QAQPGLAGPVRGVGGP+PGMMQPQ  RPP+PQ SAPPMTYPA+S    GG PV+RP
Sbjct: 119 APLIQAQPGLAGPVRGVGGPSPGMMQPQFMRPPVPQHSAPPMTYPASSAPPPGGAPVVRP 178

Query: 177 PGQMPPPVYPGQGPPMARGPPPQGPPQGFGVRPPQQFPMPPQQFGQRPMVPPPPG 231
           PGQMPP  YPGQGPPM RGPPP GP Q F  RPPQ FPMPP QF QRPM  PP G
Sbjct: 179 PGQMPPGPYPGQGPPMGRGPPPPGPLQ-FSARPPQGFPMPP-QFAQRPMGMPPQG 231

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449433521|ref|XP_004134546.1| PREDICTED: small nuclear ribonucleoprotein-associated protein B'-like [Cucumis sativus] gi|449490639|ref|XP_004158663.1| PREDICTED: small nuclear ribonucleoprotein-associated protein B'-like [Cucumis sativus]

 Score =  303 bits (776), Expect = 6e-80,   Method: Compositional matrix adjust.
 Identities = 168/191 (87%), Positives = 179/191 (93%), Gaps = 8/191 (4%)

Query: 1   MSMSKSSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNN 60
           MSMSKSSKMLQ+INYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKK  
Sbjct: 1   MSMSKSSKMLQYINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKK-- 58

Query: 61  TNEEREDRRTLGLVLLRGEEVISMTVEGPPPPEESRAKAVSASAVAGPGIGRAAGRGVPA 120
           TNEER++RRTLGLVLLRGEEVISMTVEGPPP EESRAKAV+A+A+AGPGIGRAAGRG+P 
Sbjct: 59  TNEERDERRTLGLVLLRGEEVISMTVEGPPPAEESRAKAVNAAAMAGPGIGRAAGRGIPT 118

Query: 121 APLVQAQPGLAGPVRGVGGPAPGMMQPQISRPPIPQLSAPPMTYPATSGGPPVIRPPGQM 180
           APLVQAQPGLAGPVRGVGGPAPGMMQPQISRPP+PQLSAPPMTYPA     P+IRPPGQM
Sbjct: 119 APLVQAQPGLAGPVRGVGGPAPGMMQPQISRPPVPQLSAPPMTYPAA----PIIRPPGQM 174

Query: 181 PPPVYPGQGPP 191
             P++PGQ PP
Sbjct: 175 --PMFPGQAPP 183

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356501499|ref|XP_003519562.1| PREDICTED: small nuclear ribonucleoprotein-associated protein B'-like [Glycine max]

 Score =  301 bits (772), Expect = 2e-79,   Method: Compositional matrix adjust.
 Identities = 158/181 (87%), Positives = 169/181 (93%), Gaps = 4/181 (2%)

Query: 1   MSMSKSSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNN 60
           MSMSKSSKMLQ+INYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKK  
Sbjct: 1   MSMSKSSKMLQYINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKPA 60

Query: 61  TNEEREDRRTLGLVLLRGEEVISMTVEGPPPPEESRAKAVSASAVAGPGIGRAAGRGVPA 120
              +REDRRTLGLVLLRGEEVISMTVEGPPPPEESR+KAV A+A+AGPGIGRAAGRG+P 
Sbjct: 61  EGADREDRRTLGLVLLRGEEVISMTVEGPPPPEESRSKAVGAAALAGPGIGRAAGRGIPP 120

Query: 121 APLVQAQPGLAGPVRGVGGPAPGMMQPQISRPPIPQLSAPPMTYPATSGGPPVIRPPGQM 180
           AP+VQAQPGLAGPVRGVGGPAPGMMQPQISRP  PQL+APP++YP   GGPPV+RPPGQM
Sbjct: 121 APVVQAQPGLAGPVRGVGGPAPGMMQPQISRP--PQLNAPPVSYPG--GGPPVMRPPGQM 176

Query: 181 P 181
           P
Sbjct: 177 P 177

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225463717|ref|XP_002263359.1| PREDICTED: small nuclear ribonucleoprotein-associated protein B' [Vitis vinifera] gi|147774905|emb|CAN61706.1| hypothetical protein VITISV_001610 [Vitis vinifera]

 Score =  300 bits (768), Expect = 4e-79,   Method: Compositional matrix adjust.
 Identities = 181/210 (86%), Positives = 189/210 (90%), Gaps = 11/210 (5%)

Query: 1   MSMSKSSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNN 60
           MSMSKSSKMLQ+INYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKK  
Sbjct: 1   MSMSKSSKMLQYINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKK-- 58

Query: 61  TNEEREDRRTLGLVLLRGEEVISMTVEGPPPPEESRAKAVSASAVAGPGIGRAAGRGVPA 120
            NEERE+RRTLGLVLLRGEEVISMTVEGPPPPEESRAKAV A+A+AGPGIGRAAGRG+P 
Sbjct: 59  -NEEREERRTLGLVLLRGEEVISMTVEGPPPPEESRAKAVGAAAMAGPGIGRAAGRGIPT 117

Query: 121 APLVQAQPGLAGPVRGVGGPAPGMMQPQISRPPIPQLSAPPMTYPATSGGPPVIRPPGQM 180
           APL+QAQPGLAGPVRGVGGPAPGMMQPQISRPP+PQLSAPPMTYPA     PVIRPPGQM
Sbjct: 118 APLIQAQPGLAGPVRGVGGPAPGMMQPQISRPPVPQLSAPPMTYPAA----PVIRPPGQM 173

Query: 181 PPPVYPGQGPP-MARGPPPQGPPQGFGVRP 209
           P   YPGQ PP +ARGPPP  P Q F  RP
Sbjct: 174 PG--YPGQAPPQIARGPPPPVPAQ-FAARP 200

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|118482995|gb|ABK93409.1| unknown [Populus trichocarpa]

 Score =  300 bits (768), Expect = 4e-79,   Method: Compositional matrix adjust.
 Identities = 222/272 (81%), Positives = 230/272 (84%), Gaps = 14/272 (5%)

Query: 1   MSMSKSSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNN 60
           MSMSKSSKMLQ+INYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNN
Sbjct: 1   MSMSKSSKMLQYINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNN 60

Query: 61  TNEEREDRRTLGLVLLRGEEVISMTVEGPPPPEESRAKAVSASAVAGPGIGRAAGRGVPA 120
             EEREDRRTLGLVLLRGEEVISMTVEGPPPPEESRAKAVSA+AVAGPG+GRAAGRG+P 
Sbjct: 61  --EEREDRRTLGLVLLRGEEVISMTVEGPPPPEESRAKAVSAAAVAGPGLGRAAGRGIPT 118

Query: 121 APLVQAQPGLAGPVRGVGGPAPGMMQPQISRPPIPQLSAPPMTYPATSG----GPPVIRP 176
           APLVQAQPGLAGPVRGVGGP+PGMMQPQ+SRP   QLSAPPMTYPA SG    G P++RP
Sbjct: 119 APLVQAQPGLAGPVRGVGGPSPGMMQPQLSRP---QLSAPPMTYPAGSGLPTGGAPILRP 175

Query: 177 PGQMPPPVYPGQGPPMARGPPPQGPPQGFGVRPPQQFPMPPQQFGQRPMV-PPPPGPMMR 235
           PGQMPP  Y GQG PM RGPPP GPPQ F  RPPQ FPMPPQ F QRPM  PP P   M 
Sbjct: 176 PGQMPPMPYSGQGQPMGRGPPPPGPPQ-FAARPPQGFPMPPQ-FAQRPMGGPPQPQVQMM 233

Query: 236 GPPSGPPRPGMPNAPPPRPGMPPPP--GAPVF 265
             P  PPRPGMP  PPPRPGMP PP    PVF
Sbjct: 234 RGPPAPPRPGMPAPPPPRPGMPLPPGGHVPVF 265

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356553373|ref|XP_003545031.1| PREDICTED: small nuclear ribonucleoprotein-associated protein B'-like [Glycine max]

 Score =  299 bits (766), Expect = 8e-79,   Method: Compositional matrix adjust.
 Identities = 157/181 (86%), Positives = 169/181 (93%), Gaps = 4/181 (2%)

Query: 1   MSMSKSSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNN 60
           MSMSKSSKMLQ+INYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKK  
Sbjct: 1   MSMSKSSKMLQYINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKPA 60

Query: 61  TNEEREDRRTLGLVLLRGEEVISMTVEGPPPPEESRAKAVSASAVAGPGIGRAAGRGVPA 120
              +REDRRTLGLVLLRGEEVISMTVEGPPPPEESR+KAV A+A+AGPGIGRAAGRG+P 
Sbjct: 61  EGGDREDRRTLGLVLLRGEEVISMTVEGPPPPEESRSKAVGAAALAGPGIGRAAGRGIPP 120

Query: 121 APLVQAQPGLAGPVRGVGGPAPGMMQPQISRPPIPQLSAPPMTYPATSGGPPVIRPPGQM 180
           AP+VQAQPGLAGPVRG+GGPAPGMMQPQISRP  PQL+APP++YP   GGPPV+RPPGQM
Sbjct: 121 APVVQAQPGLAGPVRGMGGPAPGMMQPQISRP--PQLNAPPVSYPG--GGPPVMRPPGQM 176

Query: 181 P 181
           P
Sbjct: 177 P 177

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224117856|ref|XP_002317685.1| predicted protein [Populus trichocarpa] gi|222860750|gb|EEE98297.1| predicted protein [Populus trichocarpa]

 Score =  297 bits (761), Expect = 3e-78,   Method: Compositional matrix adjust.
 Identities = 166/186 (89%), Positives = 174/186 (93%), Gaps = 9/186 (4%)

Query: 1   MSMSKSSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNN 60
           MSMSKSSKMLQ+INYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNN
Sbjct: 1   MSMSKSSKMLQYINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNN 60

Query: 61  TNEEREDRRTLGLVLLRGEEVISMTVEGPPPPEESRAKAVSASAVAGPGIGRAAGRGVPA 120
             EEREDRRTLGLVLLRGEEVISMTVEGPPPPEESRAKAVSA+AVAGPG+GRAAGRG+P 
Sbjct: 61  --EEREDRRTLGLVLLRGEEVISMTVEGPPPPEESRAKAVSAAAVAGPGLGRAAGRGIPT 118

Query: 121 APLVQAQPGLAGPVRGVGGPAPGMMQPQISRPPIPQLSAPPMTYPATS----GGPPVIRP 176
           APLVQAQPGLAGPVRGVGGP+PGMMQPQ+SR   PQLSAPPMTYPA S    GG P++RP
Sbjct: 119 APLVQAQPGLAGPVRGVGGPSPGMMQPQLSR---PQLSAPPMTYPAGSGLPTGGAPILRP 175

Query: 177 PGQMPP 182
           PGQMPP
Sbjct: 176 PGQMPP 181

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	286
TAIR|locus:2128610	257	smB "small nuclear ribonucleop	0.587	0.653	0.680	1.9e-51
TAIR|locus:2163416	254	AT5G44500 "AT5G44500" [Arabido	0.590	0.665	0.649	3.6e-50
UNIPROTKB|Q9PV94	240	SNRPB "Small nuclear ribonucle	0.311	0.370	0.623	2e-32
ZFIN|ZDB-GENE-040426-1819	239	snrpb "small nuclear ribonucle	0.311	0.372	0.623	2.5e-32
UNIPROTKB|P14678	240	SNRPB "Small nuclear ribonucle	0.311	0.370	0.623	2.5e-32
UNIPROTKB|Q9TU67	240	SNRPB "Small nuclear ribonucle	0.311	0.370	0.623	2.5e-32
UNIPROTKB|Q58DW4	240	SNRPB "Small nuclear ribonucle	0.311	0.370	0.623	2.5e-32
UNIPROTKB|Q9N1Q0	240	SNRPB "Small nuclear ribonucle	0.311	0.370	0.623	5.1e-32
UNIPROTKB|Q9TU66	240	SNRPB "Small nuclear ribonucle	0.311	0.370	0.612	2.2e-31
FB|FBgn0262601	199	SmB "Small ribonucleoprotein p	0.314	0.452	0.585	2.6e-30

TAIR|locus:2128610 smB "small nuclear ribonucleoprotein associated protein B" [Arabidopsis thaliana (taxid:3702)]

 Score = 534 (193.0 bits), Expect = 1.9e-51, P = 1.9e-51
 Identities = 117/172 (68%), Positives = 118/172 (68%)

Query:     1 MSMSKSSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNN 60
             MSMSKSSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKK  
Sbjct:     1 MSMSKSSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKK-- 58

Query:    61 TNEEREDRRTLGLVLLRGEEVISMTVEGPPPPEESRXXXXXXXXXXXXXXXXXXXXXXXX 120
              NEEREDRRTLGLVLLRGEEVISMTVEGPPPPEESR                        
Sbjct:    59 INEEREDRRTLGLVLLRGEEVISMTVEGPPPPEESRAKAGSAAAVAGPGIGRAAGRGVPT 118

Query:   121 XXLVQAQXXXXXXXXXXXXXXXXMMQPQISRPPIPQLSAPPMTYPATSGGPP 172
               LVQAQ                MMQPQISRPP  QLSAPP+  P     PP
Sbjct:   119 GPLVQAQPGLSGPVRGVGGPAPGMMQPQISRPP--QLSAPPIIRPPGQMLPP 168

GO:0005634 "nucleus" evidence=ISM;ISS

GO:0005732 "small nucleolar ribonucleoprotein complex" evidence=ISS

GO:0000398 "mRNA splicing, via spliceosome" evidence=TAS

GO:0005654 "nucleoplasm" evidence=IDA

GO:0015030 "Cajal body" evidence=IDA

GO:0005829 "cytosol" evidence=IDA

GO:0001510 "RNA methylation" evidence=RCA

TAIR|locus:2163416 AT5G44500 "AT5G44500" [Arabidopsis thaliana (taxid:3702)]

 Score = 522 (188.8 bits), Expect = 3.6e-50, P = 3.6e-50
 Identities = 115/177 (64%), Positives = 118/177 (66%)

Query:     1 MSMSKSSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNN 60
             MSMSKSSKMLQFINYRMRVTIQDGRQL+GKFMAFDRHMNLVLGDCEEFRKLPPAKG K  
Sbjct:     1 MSMSKSSKMLQFINYRMRVTIQDGRQLIGKFMAFDRHMNLVLGDCEEFRKLPPAKGNKK- 59

Query:    61 TNEEREDRRTLGLVLLRGEEVISMTVEGPPPPEESRXXXXXXXXXXXXXXXXXXXXXXXX 120
             TNEERE+RRTLGLVLLRGEEVISMTVEGPPPPEESR                        
Sbjct:    60 TNEEREERRTLGLVLLRGEEVISMTVEGPPPPEESRAKSGSVTAVAGPGIGRAAGRGVPT 119

Query:   121 XXLVQAQXXXXXXXXXXXXXXXXMMQPQISRPPIPQLSAPPMTYP-----ATSGGPP 172
               LVQAQ                MMQPQISRPP  Q+  PP   P     A  GGPP
Sbjct:   120 GPLVQAQPGLSGPVRGIGGPAPGMMQPQISRPP--QIIRPPGQMPPQPPFAGQGGPP 174

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISM;ISS

GO:0005732 "small nucleolar ribonucleoprotein complex" evidence=ISS

GO:0005730 "nucleolus" evidence=IDA

GO:0005829 "cytosol" evidence=RCA

UNIPROTKB|Q9PV94 SNRPB "Small nuclear ribonucleoprotein-associated protein B'" [Gallus gallus (taxid:9031)]

 Score = 305 (112.4 bits), Expect = 2.0e-32, Sum P(3) = 2.0e-32
 Identities = 58/93 (62%), Positives = 73/93 (78%)

Query:     1 MSMSKSSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNN 60
             M++ KSSKMLQ I+YRMR  +QDGR  +G F AFD+HMNL+L DC+EFRK+ P    KN+
Sbjct:     1 MTVGKSSKMLQHIDYRMRCILQDGRVFIGTFKAFDKHMNLILCDCDEFRKIKP----KNS 56

Query:    61 TNEEREDRRTLGLVLLRGEEVISMTVEGPPPPE 93
                ERE++R LGLVLLRGE ++SMTVEGPPP +
Sbjct:    57 KQPEREEKRVLGLVLLRGENLVSMTVEGPPPKD 89

GO:0003723 "RNA binding" evidence=IEA

GO:0005681 "spliceosomal complex" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

ZFIN|ZDB-GENE-040426-1819 snrpb "small nuclear ribonucleoprotein polypeptides B and B1" [Danio rerio (taxid:7955)]

 Score = 304 (112.1 bits), Expect = 2.5e-32, Sum P(3) = 2.5e-32
 Identities = 58/93 (62%), Positives = 73/93 (78%)

Query:     1 MSMSKSSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNN 60
             M++ KSSKMLQ I+YRMR  +QDGR  +G F AFD+HMNL+L DC+EFRK+ P    KN+
Sbjct:     1 MTVGKSSKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKP----KNS 56

Query:    61 TNEEREDRRTLGLVLLRGEEVISMTVEGPPPPE 93
                ERE++R LGLVLLRGE ++SMTVEGPPP +
Sbjct:    57 KQPEREEKRVLGLVLLRGENLVSMTVEGPPPKD 89

GO:0005634 "nucleus" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0030529 "ribonucleoprotein complex" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|P14678 SNRPB "Small nuclear ribonucleoprotein-associated proteins B and B'" [Homo sapiens (taxid:9606)]

 Score = 304 (112.1 bits), Expect = 2.5e-32, Sum P(3) = 2.5e-32
 Identities = 58/93 (62%), Positives = 73/93 (78%)

Query:     1 MSMSKSSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNN 60
             M++ KSSKMLQ I+YRMR  +QDGR  +G F AFD+HMNL+L DC+EFRK+ P    KN+
Sbjct:     1 MTVGKSSKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKP----KNS 56

Query:    61 TNEEREDRRTLGLVLLRGEEVISMTVEGPPPPE 93
                ERE++R LGLVLLRGE ++SMTVEGPPP +
Sbjct:    57 KQAEREEKRVLGLVLLRGENLVSMTVEGPPPKD 89

GO:0071204 "histone pre-mRNA 3'end processing complex" evidence=IEA

GO:0071208 "histone pre-mRNA DCP binding" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0005689 "U12-type spliceosomal complex" evidence=IDA

GO:0071013 "catalytic step 2 spliceosome" evidence=IDA

GO:0005683 "U7 snRNP" evidence=IDA

GO:0030532 "small nuclear ribonucleoprotein complex" evidence=TAS

GO:0005681 "spliceosomal complex" evidence=TAS

GO:0000398 "mRNA splicing, via spliceosome" evidence=IC;TAS

GO:0000387 "spliceosomal snRNP assembly" evidence=TAS

GO:0005654 "nucleoplasm" evidence=TAS

GO:0005829 "cytosol" evidence=TAS

GO:0006366 "transcription from RNA polymerase II promoter" evidence=TAS

GO:0006369 "termination of RNA polymerase II transcription" evidence=TAS

GO:0006397 "mRNA processing" evidence=TAS

GO:0008334 "histone mRNA metabolic process" evidence=TAS

GO:0008380 "RNA splicing" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0016070 "RNA metabolic process" evidence=TAS

GO:0034660 "ncRNA metabolic process" evidence=TAS

UNIPROTKB|Q9TU67 SNRPB "Small nuclear ribonucleoprotein-associated protein B'" [Erinaceus europaeus (taxid:9365)]

 Score = 304 (112.1 bits), Expect = 2.5e-32, Sum P(3) = 2.5e-32
 Identities = 58/93 (62%), Positives = 73/93 (78%)

Query:     1 MSMSKSSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNN 60
             M++ KSSKMLQ I+YRMR  +QDGR  +G F AFD+HMNL+L DC+EFRK+ P    KN+
Sbjct:     1 MTVGKSSKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKP----KNS 56

Query:    61 TNEEREDRRTLGLVLLRGEEVISMTVEGPPPPE 93
                ERE++R LGLVLLRGE ++SMTVEGPPP +
Sbjct:    57 KQAEREEKRVLGLVLLRGENLVSMTVEGPPPKD 89

GO:0005683 "U7 snRNP" evidence=ISS

UNIPROTKB|Q58DW4 SNRPB "Small nuclear ribonucleoprotein-associated protein B'" [Bos taurus (taxid:9913)]

 Score = 304 (112.1 bits), Expect = 2.5e-32, Sum P(3) = 2.5e-32
 Identities = 58/93 (62%), Positives = 73/93 (78%)

Query:     1 MSMSKSSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNN 60
             M++ KSSKMLQ I+YRMR  +QDGR  +G F AFD+HMNL+L DC+EFRK+ P    KN+
Sbjct:     1 MTVGKSSKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKP----KNS 56

Query:    61 TNEEREDRRTLGLVLLRGEEVISMTVEGPPPPE 93
                ERE++R LGLVLLRGE ++SMTVEGPPP +
Sbjct:    57 KQAEREEKRVLGLVLLRGENLVSMTVEGPPPKD 89

GO:0042802 "identical protein binding" evidence=ISS

GO:0005683 "U7 snRNP" evidence=ISS

GO:0008380 "RNA splicing" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0005681 "spliceosomal complex" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

UNIPROTKB|Q9N1Q0 SNRPB "Small nuclear ribonucleoprotein-associated protein B'" [Macropus eugenii (taxid:9315)]

 Score = 304 (112.1 bits), Expect = 5.1e-32, Sum P(3) = 5.1e-32
 Identities = 58/93 (62%), Positives = 73/93 (78%)

Query:     1 MSMSKSSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNN 60
             M++ KSSKMLQ I+YRMR  +QDGR  +G F AFD+HMNL+L DC+EFRK+ P    KN+
Sbjct:     1 MTVGKSSKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKP----KNS 56

Query:    61 TNEEREDRRTLGLVLLRGEEVISMTVEGPPPPE 93
                ERE++R LGLVLLRGE ++SMTVEGPPP +
Sbjct:    57 KQAEREEKRVLGLVLLRGENLVSMTVEGPPPKD 89

GO:0005683 "U7 snRNP" evidence=ISS

UNIPROTKB|Q9TU66 SNRPB "Small nuclear ribonucleoprotein-associated protein B'" [Monodelphis domestica (taxid:13616)]

 Score = 295 (108.9 bits), Expect = 2.2e-31, Sum P(3) = 2.2e-31
 Identities = 57/93 (61%), Positives = 72/93 (77%)

Query:     1 MSMSKSSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNN 60
             M++ KSSKMLQ I+ RMR  +QDGR  +G F AFD+HMNL+L DC+EFRK+ P    KN+
Sbjct:     1 MTVGKSSKMLQHIDCRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKP----KNS 56

Query:    61 TNEEREDRRTLGLVLLRGEEVISMTVEGPPPPE 93
                ERE++R LGLVLLRGE ++SMTVEGPPP +
Sbjct:    57 KQAEREEKRVLGLVLLRGENLVSMTVEGPPPKD 89

GO:0005683 "U7 snRNP" evidence=ISS

FB|FBgn0262601 SmB "Small ribonucleoprotein particle protein SmB" [Drosophila melanogaster (taxid:7227)]

 Score = 308 (113.5 bits), Expect = 2.6e-30, Sum P(2) = 2.6e-30
 Identities = 55/94 (58%), Positives = 74/94 (78%)

Query:     1 MSMSKSSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNN 60
             M++ K++KM+Q +NYR+R+ +QD R  +G F AFD+HMNL+LGDCEEFRK+      KN+
Sbjct:     1 MTIGKNNKMIQHLNYRVRIVLQDSRTFIGTFKAFDKHMNLILGDCEEFRKIR----SKNS 56

Query:    61 TNEEREDRRTLGLVLLRGEEVISMTVEGPPPPEE 94
                ERE++R LG VLLRGE ++S+TVEGPPPPEE
Sbjct:    57 KVPEREEKRVLGFVLLRGENIVSLTVEGPPPPEE 90

GO:0030532 "small nuclear ribonucleoprotein complex" evidence=ISS;NAS

GO:0000398 "mRNA splicing, via spliceosome" evidence=IC;ISS

GO:0005681 "spliceosomal complex" evidence=ISS

GO:0005634 "nucleus" evidence=IDA;NAS

GO:0016070 "RNA metabolic process" evidence=NAS

GO:0007052 "mitotic spindle organization" evidence=IMP

GO:0071013 "catalytic step 2 spliceosome" evidence=IDA

GO:0071011 "precatalytic spliceosome" evidence=IDA

GO:0045495 "pole plasm" evidence=IDA

GO:0007281 "germ cell development" evidence=IMP

GO:0008406 "gonad development" evidence=IMP

GO:0015030 "Cajal body" evidence=IDA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	286
cd01717	80	cd01717, Sm_B, Sm protein B	8e-58
smart00651	67	smart00651, Sm, snRNP Sm proteins	4e-22
cd06168	73	cd06168, LSMD1, LSM domain containing 1	6e-19
pfam01423	66	pfam01423, LSM, LSM domain	6e-19
cd00600	63	cd00600, Sm_like, Sm and related proteins	2e-18
COG1958	79	COG1958, LSM1, Small nuclear ribonucleoprotein (sn	7e-16
pfam09770	804	pfam09770, PAT1, Topoisomerase II-associated prote	5e-13
cd01729	89	cd01729, LSm7, Like-Sm protein 7	3e-10
cd01730	82	cd01730, LSm3, Like-Sm protein 3	3e-10
PHA03247	3151	PHA03247, PHA03247, large tegument protein UL36; P	5e-10
cd01731	69	cd01731, archaeal_Sm1, archaeal Sm protein 1	6e-10
PHA03247	3151	PHA03247, PHA03247, large tegument protein UL36; P	1e-09
PRK07764	824	PRK07764, PRK07764, DNA polymerase III subunits ga	6e-09
PRK07764	824	PRK07764, PRK07764, DNA polymerase III subunits ga	6e-09
PHA03247	3151	PHA03247, PHA03247, large tegument protein UL36; P	1e-08
PRK07764	824	PRK07764, PRK07764, DNA polymerase III subunits ga	2e-08
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	2e-08
cd01727	91	cd01727, LSm8, Like-Sm protein 8	3e-08
cd01718	79	cd01718, Sm_E, Sm protein E	6e-08
PHA03247	3151	PHA03247, PHA03247, large tegument protein UL36; P	2e-07
PRK14951	618	PRK14951, PRK14951, DNA polymerase III subunits ga	4e-07
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	5e-07
cd01728	74	cd01728, LSm1, Like-Sm protein 1	5e-07
PRK07764	824	PRK07764, PRK07764, DNA polymerase III subunits ga	1e-06
PRK12323	700	PRK12323, PRK12323, DNA polymerase III subunits ga	1e-06
PRK07764	824	PRK07764, PRK07764, DNA polymerase III subunits ga	2e-06
PTZ00138	89	PTZ00138, PTZ00138, small nuclear ribonucleoprotei	2e-06
PRK12323	700	PRK12323, PRK12323, DNA polymerase III subunits ga	3e-06
cd11678	69	cd11678, archaeal_LSm, archaeal Like-Sm protein	3e-06
cd01720	89	cd01720, Sm_D2, Sm protein D2	3e-06
PRK07764	824	PRK07764, PRK07764, DNA polymerase III subunits ga	4e-06
PRK12323	700	PRK12323, PRK12323, DNA polymerase III subunits ga	4e-06
cd01719	70	cd01719, Sm_G, Sm protein G	4e-06
pfam04652	315	pfam04652, DUF605, Vta1 like	4e-06
PRK07764	824	PRK07764, PRK07764, DNA polymerase III subunits ga	5e-06
PRK14086	617	PRK14086, dnaA, chromosomal replication initiation	5e-06
cd01739	63	cd01739, LSm11_M, Like-Sm protein 11, middle domai	8e-06
PRK00737	72	PRK00737, PRK00737, small nuclear ribonucleoprotei	1e-05
PRK14971	614	PRK14971, PRK14971, DNA polymerase III subunits ga	2e-05
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	3e-05
PHA03247	3151	PHA03247, PHA03247, large tegument protein UL36; P	4e-05
PHA03247	3151	PHA03247, PHA03247, large tegument protein UL36; P	5e-05
cd01732	76	cd01732, LSm5, Like-Sm protein 5	5e-05
cd01726	68	cd01726, LSm6, Like-Sm protein 6	6e-05
pfam05518	753	pfam05518, Totivirus_coat, Totivirus coat protein	7e-05
cd01722	69	cd01722, Sm_F, Sm protein F	7e-05
PHA03247	3151	PHA03247, PHA03247, large tegument protein UL36; P	9e-05
PRK14971	614	PRK14971, PRK14971, DNA polymerase III subunits ga	1e-04
pfam09770	804	pfam09770, PAT1, Topoisomerase II-associated prote	2e-04
PRK07764	824	PRK07764, PRK07764, DNA polymerase III subunits ga	2e-04
PRK12323	700	PRK12323, PRK12323, DNA polymerase III subunits ga	2e-04
PRK10263	1355	PRK10263, PRK10263, DNA translocase FtsK; Provisio	2e-04
PRK09111	598	PRK09111, PRK09111, DNA polymerase III subunits ga	2e-04
PHA03247	3151	PHA03247, PHA03247, large tegument protein UL36; P	3e-04
PHA03247	3151	PHA03247, PHA03247, large tegument protein UL36; P	3e-04
PRK07764	824	PRK07764, PRK07764, DNA polymerase III subunits ga	3e-04
PRK14950	585	PRK14950, PRK14950, DNA polymerase III subunits ga	3e-04
PRK06995	484	PRK06995, flhF, flagellar biosynthesis regulator F	3e-04
PHA03247	3151	PHA03247, PHA03247, large tegument protein UL36; P	4e-04
PRK07764	824	PRK07764, PRK07764, DNA polymerase III subunits ga	5e-04
PRK14951	618	PRK14951, PRK14951, DNA polymerase III subunits ga	5e-04
PRK14965	576	PRK14965, PRK14965, DNA polymerase III subunits ga	5e-04
PRK07764	824	PRK07764, PRK07764, DNA polymerase III subunits ga	6e-04
PRK14951	618	PRK14951, PRK14951, DNA polymerase III subunits ga	6e-04
pfam04652	315	pfam04652, DUF605, Vta1 like	7e-04
PRK12323	700	PRK12323, PRK12323, DNA polymerase III subunits ga	8e-04
PRK12323	700	PRK12323, PRK12323, DNA polymerase III subunits ga	9e-04
pfam04652	315	pfam04652, DUF605, Vta1 like	0.001
PRK14971	614	PRK14971, PRK14971, DNA polymerase III subunits ga	0.001
PRK03427	333	PRK03427, PRK03427, cell division protein ZipA; Pr	0.001
PRK07764	824	PRK07764, PRK07764, DNA polymerase III subunits ga	0.002
PRK12323	700	PRK12323, PRK12323, DNA polymerase III subunits ga	0.002
PRK14086	617	PRK14086, dnaA, chromosomal replication initiation	0.002
pfam05518	753	pfam05518, Totivirus_coat, Totivirus coat protein	0.002
PRK10263	1355	PRK10263, PRK10263, DNA translocase FtsK; Provisio	0.002
PRK09111	598	PRK09111, PRK09111, DNA polymerase III subunits ga	0.002
PRK14950	585	PRK14950, PRK14950, DNA polymerase III subunits ga	0.002
pfam03153	332	pfam03153, TFIIA, Transcription factor IIA, alpha/	0.002
PHA03378	991	PHA03378, PHA03378, EBNA-3B; Provisional	0.002
PRK12323	700	PRK12323, PRK12323, DNA polymerase III subunits ga	0.003
PHA03247	3151	PHA03247, PHA03247, large tegument protein UL36; P	0.004
PRK10263	1355	PRK10263, PRK10263, DNA translocase FtsK; Provisio	0.004
PRK07994	647	PRK07994, PRK07994, DNA polymerase III subunits ga	0.004
PRK07003	830	PRK07003, PRK07003, DNA polymerase III subunits ga	0.004

>gnl|CDD|212464 cd01717, Sm_B, Sm protein B

 Score =  179 bits (456), Expect = 8e-58
 Identities = 63/83 (75%), Positives = 71/83 (85%), Gaps = 3/83 (3%)

Query: 5  KSSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEE 64
          KSSKMLQ+INYRMRVT+QDGRQ VG F+AFD+HMNLVL DCEEFRK+ P K KK    EE
Sbjct: 1  KSSKMLQYINYRMRVTLQDGRQFVGTFLAFDKHMNLVLSDCEEFRKIKPKKKKK---GEE 57

Query: 65 REDRRTLGLVLLRGEEVISMTVE 87
          RE++R LGLVLLRGE V+SMTVE
Sbjct: 58 REEKRVLGLVLLRGENVVSMTVE 80

The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a hetero-heptameric ring around the Sm site of the 2,2,7-trimethyl guanosine (m3G) capped U1, U2, U4 and U5 snRNAs (Sm snRNAs) forming the core of the snRNP particle. The snRNP particle, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. Members of this family share a highly conserved Sm fold, containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Length = 80

>gnl|CDD|197820 smart00651, Sm, snRNP Sm proteins

 Score = 86.8 bits (216), Expect = 4e-22
 Identities = 25/80 (31%), Positives = 40/80 (50%), Gaps = 13/80 (16%)

Query: 7  SKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEERE 66
            + + I  R+ V +++GR+  G    FD+ MNLVL D EE  K             + E
Sbjct: 1  KFLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVK-------------DGE 47

Query: 67 DRRTLGLVLLRGEEVISMTV 86
           +R LGLV +RG  ++ + +
Sbjct: 48 KKRKLGLVFIRGNNIVYIIL 67

small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing. Length = 67

>gnl|CDD|212486 cd06168, LSMD1, LSM domain containing 1

 Score = 78.8 bits (195), Expect = 6e-19
 Identities = 26/77 (33%), Positives = 45/77 (58%), Gaps = 9/77 (11%)

Query: 11 QFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRT 70
          + +   +RVT+ DGR LVG F+  D+  N++L + EE+RK               E+ R+
Sbjct: 6  KLLGRTLRVTLTDGRVLVGTFVCTDKDGNIILSNAEEYRKPSDLGA---------EEPRS 56

Query: 71 LGLVLLRGEEVISMTVE 87
          LGLV++ G+ ++S+ V+
Sbjct: 57 LGLVMVPGKHIVSIEVD 73

The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSMD1 proteins have a single Sm-like domain structure. Sm-like proteins exist in archaea as well as prokaryotes, forming heptameric and hexameric ring structures similar to those found in eukaryotes. Length = 73

>gnl|CDD|201787 pfam01423, LSM, LSM domain

 Score = 78.4 bits (194), Expect = 6e-19
 Identities = 27/80 (33%), Positives = 39/80 (48%), Gaps = 15/80 (18%)

Query: 8  KMLQ-FINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEERE 66
          K LQ  +  R+ V +++GR+L G    FD+ MNLVL D EE  K                
Sbjct: 1  KFLQKLLGKRVTVELKNGRELRGTLKGFDQFMNLVLDDVEETIK--------------DG 46

Query: 67 DRRTLGLVLLRGEEVISMTV 86
              LGLVL+RG  ++ ++ 
Sbjct: 47 KVNKLGLVLIRGNNIVLISP 66

The LSM domain contains Sm proteins as well as other related LSM (Like Sm) proteins. The U1, U2, U4/U6, and U5 small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing contain seven Sm proteins (B/B', D1, D2, D3, E, F and G) in common, which assemble around the Sm site present in four of the major spliceosomal small nuclear RNAs. The U6 snRNP binds to the LSM (Like Sm) proteins. Sm proteins are also found in archaebacteria, which do not have any splicing apparatus suggesting a more general role for Sm proteins. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. This family also includes the bacterial Hfq (host factor Q) proteins. Hfq are also RNA-binding proteins, that form hexameric rings. Length = 66

>gnl|CDD|212462 cd00600, Sm_like, Sm and related proteins

 Score = 76.9 bits (190), Expect = 2e-18
 Identities = 29/75 (38%), Positives = 40/75 (53%), Gaps = 14/75 (18%)

Query: 11 QFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRT 70
           FI   + V ++DGR L G  +AFD++MNLVL D  E  +     GK           R 
Sbjct: 3  DFIGKTVSVELKDGRVLTGTLVAFDKYMNLVLDDVVETGR----DGKV----------RV 48

Query: 71 LGLVLLRGEEVISMT 85
          LGLVL+RG  ++S+ 
Sbjct: 49 LGLVLIRGSNIVSIR 63

The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes. Length = 63

>gnl|CDD|224869 COG1958, LSM1, Small nuclear ribonucleoprotein (snRNP) homolog [Transcription]

 Score = 70.8 bits (174), Expect = 7e-16
 Identities = 26/87 (29%), Positives = 44/87 (50%), Gaps = 11/87 (12%)

Query: 1  MSMSKSSKMLQ-FINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKN 59
          M        L+  +N R+ V +++GR+  G  + FD++MNLVL D EE            
Sbjct: 3  MLGPLPLSFLKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEIIS--------- 53

Query: 60 NTNEEREDRRTLGLVLLRGEEVISMTV 86
            + E+  RR  G VL+RG+ ++ ++ 
Sbjct: 54 -HDGEKNVRRLGGEVLIRGDNIVLISP 79

Length = 79

>gnl|CDD|220392 pfam09770, PAT1, Topoisomerase II-associated protein PAT1

 Score = 68.6 bits (168), Expect = 5e-13
 Identities = 43/206 (20%), Positives = 53/206 (25%), Gaps = 9/206 (4%)

Query: 88  GPPPPEESRAKAVSASAVAGPGIGRAAG------RGVPAAPLVQAQPGLAGPVRGVGGPA 141
           G  P  E +      S        +           +         P     V   G P 
Sbjct: 127 GTAPKPEPQPPQAPESQPQPQTPAQKMLSLEEVEAQLQQRQQAPQLPQPPQQVLPQGMPP 186

Query: 142 PGMMQPQISRPPIP-QLSAPPMTYPATSGGPPVIRPPGQMPPPVYPGQGPPMARGPPPQG 200
                PQ   P  P     PP  +P        +  P Q P         P    P  Q 
Sbjct: 187 RQAAFPQQGPPEQPPGYPQPPQGHPEQVQPQQFLPAPSQAPAQPPLPPQLPQQPPPLQQP 246

Query: 201 PPQGFGVRPPQQFPMPPQQFGQRPMVPPPPGPMMRGPPSGPPRPGMPNAPPPRPGMPPPP 260
              G   + P   P PPQQ  Q P     P P     P+  P        P  P   P  
Sbjct: 247 QFPGLSQQMPPPPPQPPQQQQQPPQPQAQPPPQN--QPTPHPGLPQGQNAPLPPPQQPQL 304

Query: 261 GAPVFRPGMPPPPPNAQQQQQNQQQQ 286
              V +P      P  ++Q     QQ
Sbjct: 305 LPLVQQPQGQQRGPQFREQLVQLSQQ 330

Members of this family are necessary for accurate chromosome transmission during cell division. Length = 804

>gnl|CDD|212476 cd01729, LSm7, Like-Sm protein 7

 Score = 55.7 bits (135), Expect = 3e-10
 Identities = 26/80 (32%), Positives = 46/80 (57%), Gaps = 7/80 (8%)

Query: 11 QFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRT 70
          ++++ ++RV  Q GR++ G    +D+ +NLVL D  E+  L   +     T+E     R+
Sbjct: 9  KYVDKKIRVKFQGGREVTGILKGYDQLLNLVLDDTVEY--LRDPEDPYKLTDET----RS 62

Query: 71 LGLVLLRGEEVISMT-VEGP 89
          LGLV+ RG  V+ ++ V+G 
Sbjct: 63 LGLVVCRGTSVVLISPVDGT 82

The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a hetero-heptameric ring around the 3'-terminus uridylation tag of the gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA. LSm2-8 form the core of the snRNP particle that, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. LSm1-7 is involved in recognition of the 3' uridylation tag and recruitment of the decapping machinery. LSm657 is believed to be an assembly intermediate for both the LSm1-7 and LSm2-8 rings. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Length = 89

>gnl|CDD|212477 cd01730, LSm3, Like-Sm protein 3

 Score = 55.3 bits (134), Expect = 3e-10
 Identities = 22/69 (31%), Positives = 39/69 (56%), Gaps = 5/69 (7%)

Query: 16 RMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEE--REDRRTLGL 73
          R+ V ++  R+L G+  A+D+H+N++LGD EE             T EE  +  +R + +
Sbjct: 13 RVYVKLRGDRELRGRLHAYDQHLNMILGDVEETITTVE---IDEETYEEIYKTTKRNIPM 69

Query: 74 VLLRGEEVI 82
          + +RG+ VI
Sbjct: 70 LFVRGDGVI 78

The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a hetero-heptameric ring around the 3'-terminus uridylation tag of the gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA. LSm2-8 form the core of the snRNP particle that, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. LSm1-7 is involved in recognition of the 3' uridylation tag and recruitment of the decapping machinery. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Length = 82

>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional

 Score = 60.0 bits (145), Expect = 5e-10
 Identities = 57/205 (27%), Positives = 64/205 (31%), Gaps = 8/205 (3%)

Query: 89   PPPPEESRAKAVSASAVAGPGIGRAAGRGVPAAPLVQAQPG--LAGPVRGVGGPAPGMMQ 146
            P  P      AV A      G  R A     A P   A P    AGP R +  PA   + 
Sbjct: 2733 PALPAAPAPPAVPAGPATPGGPARPARPPTTAGPPAPAPPAAPAAGPPRRLTRPAVASLS 2792

Query: 147  PQISRPPIPQLSAPP--MTYPATSGGPPVIRPPGQMPPPVYPGQ-GPPMARGPPPQGPPQ 203
                  P P   A P        +  PP   P G +PPP       PP   GPPP   P 
Sbjct: 2793 ESRESLPSPWDPADPPAAVLAPAAALPPAASPAGPLPPPTSAQPTAPPPPPGPPPPSLPL 2852

Query: 204  GFGVRPPQQFPM--PPQQFGQRPMVPPPPGPMMRGPPSGPPRPGMPNAPPPRPGMPPPPG 261
            G  V P        P +    +P  P  P P+ R       R     A PP     PP  
Sbjct: 2853 GGSVAPGGDVRRRPPSRSPAAKPAAPARP-PVRRLARPAVSRSTESFALPPDQPERPPQP 2911

Query: 262  APVFRPGMPPPPPNAQQQQQNQQQQ 286
                 P   P PP   Q Q      
Sbjct: 2912 QAPPPPQPQPQPPPPPQPQPPPPPP 2936

Length = 3151

>gnl|CDD|212478 cd01731, archaeal_Sm1, archaeal Sm protein 1

 Score = 54.1 bits (131), Expect = 6e-10
 Identities = 23/75 (30%), Positives = 38/75 (50%), Gaps = 14/75 (18%)

Query: 9  MLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDR 68
          + + +N  + V ++ G+++ G    FD+H+NLVL + EE                E E  
Sbjct: 6  LNESLNKNVLVKLKGGKEVRGVLKGFDQHLNLVLENAEEII--------------EGESV 51

Query: 69 RTLGLVLLRGEEVIS 83
          R LG VL+RG+ V+ 
Sbjct: 52 RKLGTVLVRGDNVVF 66

The archaeal Sm1 proteins: The Sm proteins are conserved in all three domains of life and are always associated with U-rich RNA sequences. They function to mediate RNA-RNA interactions and RNA biogenesis. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. Eukaryotic Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6). Since archaebacteria do not have any splicing apparatus, their Sm proteins may play a more general role. Archaeal LSm proteins are likely to represent the ancestral Sm domain. Length = 69

>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional

 Score = 58.8 bits (142), Expect = 1e-09
 Identities = 48/193 (24%), Positives = 61/193 (31%), Gaps = 8/193 (4%)

Query: 88   GPPPPEESRAKAVSASAV--AGPGIGRAAGRGVPAAPLVQAQPGLAGPVRGVGGPAPGMM 145
              PP   +R    S S    + P     A           A P  A P   +  P     
Sbjct: 2777 AGPPRRLTRPAVASLSESRESLPSPWDPADPPAAVLAPAAALPPAASPAGPLP-PPTSAQ 2835

Query: 146  QPQISRPPIPQLSAPPMTYPATSGGPPVIRPPGQMPPPVYPGQGPPMARGPPPQGPPQGF 205
                  PP P   + P+      GG    RPP + P        P     PP +   +  
Sbjct: 2836 PTAPPPPPGPPPPSLPLGGSVAPGGDVRRRPPSRSPAAK-----PAAPARPPVRRLARPA 2890

Query: 206  GVRPPQQFPMPPQQFGQRPMVPPPPGPMMRGPPSGPPRPGMPNAPPPRPGMPPPPGAPVF 265
              R  + F +PP Q  + P    PP P  +  P  PP+P  P  PPPRP  P  P     
Sbjct: 2891 VSRSTESFALPPDQPERPPQPQAPPPPQPQPQPPPPPQPQPPPPPPPRPQPPLAPTTDPA 2950

Query: 266  RPGMPPPPPNAQQ 278
              G P        
Sbjct: 2951 GAGEPSGAVPQPW 2963

Length = 3151

>gnl|CDD|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau; Validated

 Score = 56.1 bits (136), Expect = 6e-09
 Identities = 31/177 (17%), Positives = 40/177 (22%)

Query: 88  GPPPPEESRAKAVSASAVAGPGIGRAAGRGVPAAPLVQAQPGLAGPVRGVGGPAPGMMQP 147
            P  P    A A + +A A      A   GV A         +     G  G        
Sbjct: 617 APAAPAAPAAPAPAGAAAAPAEASAAPAPGVAAPEHHPKHVAVPDASDGGDGWPAKAGGA 676

Query: 148 QISRPPIPQLSAPPMTYPATSGGPPVIRPPGQMPPPVYPGQGPPMARGPPPQGPPQGFGV 207
             + PP     A P      +   P   P    P            +       P     
Sbjct: 677 APAAPPPAPAPAAPAAPAGAAPAQPAPAPAATPPAGQADDPAAQPPQAAQGASAPSPAAD 736

Query: 208 RPPQQFPMPPQQFGQRPMVPPPPGPMMRGPPSGPPRPGMPNAPPPRPGMPPPPGAPV 264
            P    P P            PP P    P + P     P+ P     M       +
Sbjct: 737 DPVPLPPEPDDPPDPAGAPAQPPPPPAPAPAAAPAAAPPPSPPSEEEEMAEDDAPSM 793

Length = 824

>gnl|CDD|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau; Validated

 Score = 56.1 bits (136), Expect = 6e-09
 Identities = 36/191 (18%), Positives = 41/191 (21%)

Query: 96  RAKAVSASAVAGPGIGRAAGRGVPAAPLVQAQPGLAGPVRGVGGPAPGMMQPQISRPPIP 155
            A    A   AG     A     P     +     A        PA     P  +     
Sbjct: 585 EAVVGPAPGAAGGEGPPAPASSGPPEEAARPAAPAAPAAPAAPAPAGAAAAPAEASAAPA 644

Query: 156 QLSAPPMTYPATSGGPPVIRPPGQMPPPVYPGQGPPMARGPPPQGPPQGFGVRPPQQFPM 215
              A P  +P     P         P              P P  P    G  P Q  P 
Sbjct: 645 PGVAAPEHHPKHVAVPDASDGGDGWPAKAGGAAPAAPPPAPAPAAPAAPAGAAPAQPAPA 704

Query: 216 PPQQFGQRPMVPPPPGPMMRGPPSGPPRPGMPNAPPPRPGMPPPPGAPVFRPGMPPPPPN 275
           P           P   P      +  P P   +  P  P    PP         PPPP  
Sbjct: 705 PAATPPAGQADDPAAQPPQAAQGASAPSPAADDPVPLPPEPDDPPDPAGAPAQPPPPPAP 764

Query: 276 AQQQQQNQQQQ 286
           A          
Sbjct: 765 APAAAPAAAPP 775

Length = 824

>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional

 Score = 55.3 bits (133), Expect = 1e-08
 Identities = 54/205 (26%), Positives = 70/205 (34%), Gaps = 14/205 (6%)

Query: 87   EGPPPPEESRAKAVSASAVAGPGIGRAAGRGVPA-APLVQAQPGLAGPVRGVGGPAPGMM 145
               P    + A   + +  A P  G       PA A L +++  L  P      PA   +
Sbjct: 2754 PARPARPPTTAGPPAPAPPAAPAAGPPRRLTRPAVASLSESRESLPSPWDPADPPAA--V 2811

Query: 146  QPQISRPPIPQLSAPPMTYPATSGGPPVIRPPGQMPPPVYPG----QGPPMARGPPPQGP 201
                +  P     A P+  P ++       PPG  PP +  G     G  + R PP + P
Sbjct: 2812 LAPAAALPPAASPAGPLPPPTSAQPTAPPPPPGPPPPSLPLGGSVAPGGDVRRRPPSRSP 2871

Query: 202  PQGFGVRPPQQFPMPPQQFGQRPMVPPPPGPMMRGPPSGPPRPGMPNAPPPRPGMPPPPG 261
                    P     PP +   RP V          PP  P RP  P APPP    P PP 
Sbjct: 2872 AA-----KPAAPARPPVRRLARPAVSRSTESFAL-PPDQPERPPQPQAPPPPQPQPQPPP 2925

Query: 262  APVFRPGMPPPP-PNAQQQQQNQQQ 285
             P  +P  PPPP P           
Sbjct: 2926 PPQPQPPPPPPPRPQPPLAPTTDPA 2950

Length = 3151

>gnl|CDD|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau; Validated

 Score = 54.6 bits (132), Expect = 2e-08
 Identities = 41/197 (20%), Positives = 47/197 (23%), Gaps = 8/197 (4%)

Query: 88  GPPPPEESRAKAVSASAVAGPGIGRAAGRGVPAAPLVQAQPGLAGPVRGVGGPAPGMMQP 147
           G    E   A A S            A    PAAP                 P     + 
Sbjct: 593 GAAGGEGPPAPASSGPPEEAARPAAPAAPAAPAAPAPAGAAAAPAEASAAPAPGVAAPEH 652

Query: 148 QISRPPIPQLSAPPMTYPATSGGPPVIRPPGQMPPPVYPGQGPPMARGP---PPQGPPQG 204
                 +P  S     +PA +GG     PP    P             P   P   PP G
Sbjct: 653 HPKHVAVPDASDGGDGWPAKAGGAAPAAPPPAPAPAAPAAPAGAAPAQPAPAPAATPPAG 712

Query: 205 FGVRPPQQFPMPPQQFGQRP-----MVPPPPGPMMRGPPSGPPRPGMPNAPPPRPGMPPP 259
               P  Q P   Q            VP PP P     P+G P    P   P     P  
Sbjct: 713 QADDPAAQPPQAAQGASAPSPAADDPVPLPPEPDDPPDPAGAPAQPPPPPAPAPAAAPAA 772

Query: 260 PGAPVFRPGMPPPPPNA 276
              P           + 
Sbjct: 773 APPPSPPSEEEEMAEDD 789

Length = 824

>gnl|CDD|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1, 2, 3, 4 family

 Score = 54.8 bits (132), Expect = 2e-08
 Identities = 30/105 (28%), Positives = 35/105 (33%), Gaps = 7/105 (6%)

Query: 187 GQGPPMARGPPPQGPPQGFGVRPPQQFPMPPQQFGQRPMVPPPPGPMMRGPPSGPPRPGM 246
            Q  P  R  P   P  G   +PP     P QQF  +P+    P   M   P GP  P  
Sbjct: 376 MQLQPRMRQLPMGSPMGGAMGQPPYYGQGPQQQFNGQPLG--WPRMSMMPTPMGPGGPLR 433

Query: 247 PNAPPPRPGMPPPPGAPVFRPGMPPP-----PPNAQQQQQNQQQQ 286
           PN   P   +  P          PP      PPN Q    +Q   
Sbjct: 434 PNGLAPMNAVRAPSRNAQNAAQKPPMQPVMYPPNYQSLPLSQDLP 478

These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis (GP:11610605_PABP3 ), platelets (SP:Q13310_PABP4 ), broadly expressed (SP:P11940_PABP1) and of unknown tissue range (SP:Q15097_PABP2). Length = 562

>gnl|CDD|212474 cd01727, LSm8, Like-Sm protein 8

 Score = 49.8 bits (120), Expect = 3e-08
 Identities = 29/76 (38%), Positives = 39/76 (51%), Gaps = 10/76 (13%)

Query: 6  SSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEER 65
          SS +  ++N R+ V   DGR +VG    FD+  NL+L +C E R     +G      EE 
Sbjct: 1  SSLLEDYLNKRVVVITTDGRVIVGTLKGFDQTTNLILSNCHE-RVYSSDEG-----VEEV 54

Query: 66 EDRRTLGLVLLRGEEV 81
               LGL LLRG+ V
Sbjct: 55 P----LGLYLLRGDNV 66

The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a hetero-heptameric ring around the 3'-terminus uridylation tag of the gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA. LSm2-8 form the core of the snRNP particle that, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. LSm1-7 is involved in recognition of the 3' uridylation tag and recruitment of the decapping machinery. LSm657 is believed to be an assembly intermediate for both the LSm1-7 and LSm2-8 rings. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Length = 91

>gnl|CDD|212465 cd01718, Sm_E, Sm protein E

 Score = 48.7 bits (117), Expect = 6e-08
 Identities = 29/87 (33%), Positives = 41/87 (47%), Gaps = 24/87 (27%)

Query: 9  MLQFINY-------RMRVTI----QDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGK 57
          M+Q IN        + RV I    Q   ++ GK + FD +MNLVL D EE          
Sbjct: 4  MVQPINLIFRYLQNKSRVQIWLYEQTDMRIEGKIIGFDEYMNLVLDDAEE-------VHL 56

Query: 58 KNNTNEEREDRRTLGLVLLRGEEVISM 84
          K NT      R+ LG +LL+G+ +  +
Sbjct: 57 KTNT------RKPLGRILLKGDNITLI 77

The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a hetero-heptameric ring around the Sm site of the 2,2,7-trimethyl guanosine (m3G) capped U1, U2, U4 and U5 snRNAs (Sm snRNAs) forming the core of the snRNP particle. The snRNP particle, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit E binds subunits F and G to form a trimer which then assembles onto snRNA along with the D1/D2 and D3/B heterodimers forming a seven-membered ring structure. Length = 79

>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional

 Score = 51.9 bits (124), Expect = 2e-07
 Identities = 51/193 (26%), Positives = 60/193 (31%), Gaps = 16/193 (8%)

Query: 89   PPPPEESRAKAVSASAVAGPGIGRAAGRGVPAAPLVQAQPGLAGPVRGV----GGPAPGM 144
            P  P +  A  ++ +A   P    A     P +    A P   GP        G  APG 
Sbjct: 2801 PWDPADPPAAVLAPAAALPPAASPAGPLPPPTSAQPTAPPPPPGPPPPSLPLGGSVAPG- 2859

Query: 145  MQPQISRPPIPQLSAPPMTYPATSGGPPV---IRPPGQMPPPVYPGQGPPMARGPPPQGP 201
                  RPP    S  P   PA    PPV    RP        +        R P PQ P
Sbjct: 2860 -GDVRRRPP----SRSPAAKPAAPARPPVRRLARPAVSRSTESFALPPDQPERPPQPQAP 2914

Query: 202  PQGFGVRPPQQFPMPPQQFGQRPMVPPPPGPMMRGPPSGPPRPGMPNAPPPRPGMPPPPG 261
            P       P   P P       P   PP  P      +G P   +P    P  G   P  
Sbjct: 2915 PPPQPQPQPPPPPQPQPPPPPPPRPQPPLAPTTDPAGAGEPSGAVPQ---PWLGALVPGR 2971

Query: 262  APVFRPGMPPPPP 274
              V R  +P P P
Sbjct: 2972 VAVPRFRVPQPAP 2984

Length = 3151

>gnl|CDD|237865 PRK14951, PRK14951, DNA polymerase III subunits gamma and tau; Provisional

 Score = 50.9 bits (122), Expect = 4e-07
 Identities = 21/132 (15%), Positives = 28/132 (21%), Gaps = 7/132 (5%)

Query: 138 GGPAPGMMQPQISRPPIPQLSAPPMTYPATSGGPPVIRPPGQMPPPVYP-GQGPPMARGP 196
              A    + +    P     A      A +   P   P      P  P    PP     
Sbjct: 369 AAEAAAPAEKKTPARPEAAAPAAAPVAQAAAAPAPAAAPAAAASAPAAPPAAAPPAPVAA 428

Query: 197 PPQGPPQGFGVRPPQQFPMPPQQFGQRPMVPPPPGPMMRGPPSGPPRPGMPNAPPPRPGM 256
           P    P       P    + P                +  P    P P + +A P     
Sbjct: 429 PAAAAPAAAPAAAPAAVALAPAPP------AQAAPETVAIPVRVAPEPAVASAAPAPAAA 482

Query: 257 PPPPGAPVFRPG 268
           P          G
Sbjct: 483 PAAARLTPTEEG 494

Length = 618

>gnl|CDD|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1, 2, 3, 4 family

 Score = 50.2 bits (120), Expect = 5e-07
 Identities = 26/116 (22%), Positives = 35/116 (30%), Gaps = 10/116 (8%)

Query: 174 IRPPG---QMPPPVYPGQGPPMARGPPPQ----GPPQGFGVRPPQQFPMPPQQFGQRPMV 226
           ++P      M  P+    G P   G  PQ    G P G+        PM P     RP  
Sbjct: 378 LQPRMRQLPMGSPMGGAMGQPPYYGQGPQQQFNGQPLGWPRMSMMPTPMGPGG-PLRPNG 436

Query: 227 PPPPGPMMRGPPSGPPRPGMPNAPPPRPGMPPPPGAPVFRPGMPPPPPNAQQQQQN 282
             P   +     +            P    P     P+ +  +P P   A Q  QN
Sbjct: 437 LAPMNAVRAPSRNAQNAAQ-KPPMQPVMYPPNYQSLPLSQD-LPQPQSTASQGGQN 490

These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis (GP:11610605_PABP3 ), platelets (SP:Q13310_PABP4 ), broadly expressed (SP:P11940_PABP1) and of unknown tissue range (SP:Q15097_PABP2). Length = 562

>gnl|CDD|212475 cd01728, LSm1, Like-Sm protein 1

 Score = 46.0 bits (110), Expect = 5e-07
 Identities = 21/74 (28%), Positives = 38/74 (51%), Gaps = 11/74 (14%)

Query: 9  MLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDR 68
          + + ++ ++ V ++DGR+L+G   +FD+  NLVL D  E          +     +  D 
Sbjct: 7  LEEELDKKILVVLRDGRKLIGILRSFDQFANLVLEDTVE----------RIIVGNQYGDI 56

Query: 69 RTLGLVLLRGEEVI 82
             GL ++RGE V+
Sbjct: 57 P-RGLFIIRGENVV 69

The eukaryotic LSm proteins (LSm1-7) assemble into a hetero-heptameric ring around the 3'-terminus of the gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA. Accumulation of uridylated RNAs in an lsm1 mutant suggests an involvement of the LSm1-7 complex in recognition of the 3' uridylation tag and recruitment of the decapping machinery. LSm1-7, together with Pat1, are also called the decapping activator. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Length = 74

>gnl|CDD|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau; Validated

 Score = 49.6 bits (119), Expect = 1e-06
 Identities = 27/147 (18%), Positives = 29/147 (19%), Gaps = 4/147 (2%)

Query: 134 VRGVGGPAPGMMQPQISRPPIPQLSAPPMTYPATSGGPPVIRPPGQMPPPVYPGQGPPMA 193
           V  V GPAPG    +    P           PA    P    P    P           A
Sbjct: 584 VEAVVGPAPGAAGGEGPPAPASSGPPEEAARPAAPAAPA--APAAPAPAGAAAAPAEASA 641

Query: 194 RGPPPQGPPQGFGVRPPQQFPMPPQQFGQRPMVPPPPGPMMRGPPSGPPRPGMPNAPPPR 253
              P    P+                          P      P    P    P    P 
Sbjct: 642 APAPGVAAPEHHPKHVAVPDASDGGDGWPAKAGGAAPAAPPPAPAPAAPAA--PAGAAPA 699

Query: 254 PGMPPPPGAPVFRPGMPPPPPNAQQQQ 280
              P P   P       P     Q  Q
Sbjct: 700 QPAPAPAATPPAGQADDPAAQPPQAAQ 726

Length = 824

>gnl|CDD|237057 PRK12323, PRK12323, DNA polymerase III subunits gamma and tau; Provisional

 Score = 49.5 bits (118), Expect = 1e-06
 Identities = 33/198 (16%), Positives = 40/198 (20%), Gaps = 5/198 (2%)

Query: 87  EGPPPPEESRAKAVSASAVAGPGIGRAAGRGVPAAPLVQAQPGLAGPVRGVGG----PAP 142
              P    +   A  A A A P     A    PAAP        A            PAP
Sbjct: 371 GAGPATAAAAPVAQPAPAAAAPAAAAPAPAAPPAAPAAAPAAAAAARAVAAAPARRSPAP 430

Query: 143 GMMQPQISRPPIPQLSAP-PMTYPATSGGPPVIRPPGQMPPPVYPGQGPPMARGPPPQGP 201
             +             AP P   PA +             P        P    P     
Sbjct: 431 EALAAARQASARGPGGAPAPAPAPAAAPAAAARPAAAGPRPVAAAAAAAPARAAPAAAPA 490

Query: 202 PQGFGVRPPQQFPMPPQQFGQRPMVPPPPGPMMRGPPSGPPRPGMPNAPPPRPGMPPPPG 261
           P      P ++ P              P G +    P               P     P 
Sbjct: 491 PADDDPPPWEELPPEFASPAPAQPDAAPAGWVAESIPDPATADPDDAFETLAPAPAAAPA 550

Query: 262 APVFRPGMPPPPPNAQQQ 279
                   P   P   + 
Sbjct: 551 PRAAAATEPVVAPRPPRA 568

Length = 700

>gnl|CDD|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau; Validated

 Score = 48.4 bits (116), Expect = 2e-06
 Identities = 39/177 (22%), Positives = 50/177 (28%), Gaps = 6/177 (3%)

Query: 87  EGPPPPEESRAKAVSASAVAGPGIGRAAGRGVPAAPLVQAQPGLAGPVRGVGGPAPGMMQ 146
             P P   + A A +++A A             A P             G   PA     
Sbjct: 625 AAPAPAGAAAAPAEASAAPAPGVAAPEHHPKHVAVPDASDGGDGWPAKAGGAAPAAPPPA 684

Query: 147 PQISRPPIPQLSAPPMTYPATSGGPPVIRPPGQMPPPVYPGQGPPMARGPPPQGPPQGFG 206
           P  + P  P  +AP    PA +  PP  +       P    QG       P         
Sbjct: 685 PAPAAPAAPAGAAPAQPAPAPAATPPAGQADDPAAQPPQAAQG----ASAPSPAADD--P 738

Query: 207 VRPPQQFPMPPQQFGQRPMVPPPPGPMMRGPPSGPPRPGMPNAPPPRPGMPPPPGAP 263
           V  P +   PP   G     PPPP P     P+  P P  P+          P    
Sbjct: 739 VPLPPEPDDPPDPAGAPAQPPPPPAPAPAAAPAAAPPPSPPSEEEEMAEDDAPSMDD 795

Length = 824

>gnl|CDD|185472 PTZ00138, PTZ00138, small nuclear ribonucleoprotein; Provisional

 Score = 45.1 bits (107), Expect = 2e-06
 Identities = 27/95 (28%), Positives = 41/95 (43%), Gaps = 27/95 (28%)

Query: 1  MSMSK---SSKMLQFINY-------RMRVTI----QDGRQLVGKFMAFDRHMNLVLGDCE 46
          M M+K      M Q IN        + RV I        ++ GK + FD +MN+VL D E
Sbjct: 1  MMMTKRKLQKIMTQPINQIFRFFTEKTRVQIWLYDHPNLRIEGKILGFDEYMNMVLDDAE 60

Query: 47 EFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEV 81
          E                ++  R+ LG +LL+G+ +
Sbjct: 61 EV-------------YTKKNTRKDLGRILLKGDNI 82

Length = 89

>gnl|CDD|237057 PRK12323, PRK12323, DNA polymerase III subunits gamma and tau; Provisional

 Score = 47.9 bits (114), Expect = 3e-06
 Identities = 40/199 (20%), Positives = 47/199 (23%), Gaps = 13/199 (6%)

Query: 92  PEESRAKAVSASAVAGPGIGRAAGRGVPAAPLVQAQPGLAGPVRGVGGPAPGMMQPQISR 151
           P +S   A  A+A A P    A     PAA         A P       A          
Sbjct: 365 PGQSGGGAGPATAAAAPVAQPAPAAAAPAAAAPAPAAPPAAPAAAPAAAAAARAVAAAPA 424

Query: 152 PPIPQLSAPPMTYPATSGGPPVIRPPGQMPPPVYPGQGPPMARGP--------PPQGPPQ 203
              P   A      A++ GP     P   P         P A GP               
Sbjct: 425 RRSPAPEALAAARQASARGPGGAPAPAPAPAAAPAAAARPAAAGPRPVAAAAAAAPARAA 484

Query: 204 GFGVRPPQQFPMPPQQFGQRPMVPPPPGPMMRGPP----SGPPRPGMPNAPPPRPGM-PP 258
                 P     PP +        P P      P        P P   +       + P 
Sbjct: 485 PAAAPAPADDDPPPWEELPPEFASPAPAQPDAAPAGWVAESIPDPATADPDDAFETLAPA 544

Query: 259 PPGAPVFRPGMPPPPPNAQ 277
           P  AP  R      P  A 
Sbjct: 545 PAAAPAPRAAAATEPVVAP 563

Length = 700

>gnl|CDD|212489 cd11678, archaeal_LSm, archaeal Like-Sm protein

 Score = 43.7 bits (103), Expect = 3e-06
 Identities = 25/79 (31%), Positives = 39/79 (49%), Gaps = 15/79 (18%)

Query: 8  KMLQFINYRMRVTIQ-DGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEERE 66
          K+   +  R+RV ++ D  QL G+ +A D +MNL L D  E               EE+ 
Sbjct: 4  KVKSLVGSRIRVEMKGDENQLQGRLVAVDDYMNLHLTDTMEC------------VGEEKV 51

Query: 67 DRRTLGLVLLRGEEVISMT 85
            R+LG V+LRG  ++ + 
Sbjct: 52 --RSLGTVVLRGNNILLIQ 68

The archaeal Sm-like (LSm): The Sm proteins are conserved in all three domains of life and are always associated with U-rich RNA sequences. They function to mediate RNA-RNA interactions and RNA biogenesis. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. Eukaryotic Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6). Since archaebacteria do not have any splicing apparatus, their Sm proteins may play a more general role. Archaeal LSm proteins are likely to represent the ancestral Sm domain. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes. Length = 69

>gnl|CDD|212467 cd01720, Sm_D2, Sm protein D2

 Score = 44.2 bits (105), Expect = 3e-06
 Identities = 23/71 (32%), Positives = 35/71 (49%), Gaps = 7/71 (9%)

Query: 12 FINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTL 71
           IN R      + ++L+ +  AFDRH N+VL + +E     P  GK   +    +DR   
Sbjct: 20 LINCR------NNKKLLARVKAFDRHCNMVLENVKEMWTEVPKTGKGKKSKPVNKDRFIS 73

Query: 72 GLVLLRGEEVI 82
           +  LRG+ VI
Sbjct: 74 KM-FLRGDSVI 83

The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a hetero-heptameric ring around the Sm site of the 2,2,7-trimethyl guanosine (m3G) capped U1, U2, U4 and U5 snRNAs (Sm snRNAs) forming the core of the snRNP particle. The snRNP particle, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D2 heterodimerizes with subunit D1 and three such heterodimers form a hexameric ring structure with alternating D1 and D2 subunits. The D1 - D2 heterodimer also assembles into a heptameric ring containing D2, D3, E, F, and G subunits. Length = 89

>gnl|CDD|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau; Validated

 Score = 47.7 bits (114), Expect = 4e-06
 Identities = 25/110 (22%), Positives = 28/110 (25%), Gaps = 1/110 (0%)

Query: 155 PQLSAPPMTYPATSGGPPVIRPPGQMPPPVYPGQGPPMARGPPPQGPPQGFGVRPPQQFP 214
           P  +AP     A +  P              P   P  A  P P   P       P    
Sbjct: 394 PAAAAPSAAAAAPAAAPAPAAAAPAAAAAPAPAAAPQPAPAPAPAPAPPSPAGNAPAGGA 453

Query: 215 MPPQQFGQRPMVP-PPPGPMMRGPPSGPPRPGMPNAPPPRPGMPPPPGAP 263
             P         P P P        +  P P    AP   P  P  P AP
Sbjct: 454 PSPPPAAAPSAQPAPAPAAAPEPTAAPAPAPPAAPAPAAAPAAPAAPAAP 503

Length = 824

>gnl|CDD|237057 PRK12323, PRK12323, DNA polymerase III subunits gamma and tau; Provisional

 Score = 47.6 bits (113), Expect = 4e-06
 Identities = 43/194 (22%), Positives = 54/194 (27%), Gaps = 23/194 (11%)

Query: 86  VEGPPPPEESRAKAVSASAVAGPGIGRAAGRGVPAAPLVQAQPGLAGPVRGVGGPAPGMM 145
               P    +   A  A+A A   +  A  R  PA   + A    A      G PAP   
Sbjct: 395 AAPAPAAPPAAPAAAPAAAAAARAVAAAPARRSPAPEALAAARQ-ASARGPGGAPAP--- 450

Query: 146 QPQISRPPIPQLSAPPMTYPATSGGPPVIRPPGQMPPPVYPGQGPPMARGPPPQGPPQGF 205
                  P P  +      PA +G  PV       P        P  A  P    PP   
Sbjct: 451 ------APAPAAAPAAAARPAAAGPRPVAAAAAAAPAR----AAPAAAPAPADDDPP--- 497

Query: 206 GVRPPQQFPMPPQQFGQRPMVPPPPGPMMRG---PPSGPPRPGMPNAPPPRPGMPPPPGA 262
              P ++ P              P G +      P +  P        P     P P  A
Sbjct: 498 ---PWEELPPEFASPAPAQPDAAPAGWVAESIPDPATADPDDAFETLAPAPAAAPAPRAA 554

Query: 263 PVFRPGMPPPPPNA 276
               P + P PP A
Sbjct: 555 AATEPVVAPRPPRA 568

Length = 700

>gnl|CDD|212466 cd01719, Sm_G, Sm protein G

 Score = 43.7 bits (104), Expect = 4e-06
 Identities = 19/73 (26%), Positives = 34/73 (46%), Gaps = 14/73 (19%)

Query: 12 FINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTL 71
          +++ R+ + +   R++ G    FD  MNLVL D  E        G+K            +
Sbjct: 8  YMDKRLSLKLNGNRKVSGVLRGFDPFMNLVLDDAVEEVG----DGEKTP----------I 53

Query: 72 GLVLLRGEEVISM 84
          G+V++RG  +I +
Sbjct: 54 GMVVIRGNSIIMI 66

The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a hetero-heptameric ring around the Sm site of the 2,2,7-trimethyl guanosine (m3G) capped U1, U2, U4 and U5 snRNAs (Sm snRNAs) forming the core of the snRNP particle. The snRNP particle, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit G binds subunits E and F to form a trimer which then assembles onto snRNA along with the D1/D2 and D3/B heterodimers forming a seven-membered ring structure. Length = 70

>gnl|CDD|218191 pfam04652, DUF605, Vta1 like

 Score = 47.0 bits (112), Expect = 4e-06
 Identities = 22/105 (20%), Positives = 25/105 (23%), Gaps = 12/105 (11%)

Query: 182 PPVYPGQGPPMARGPPPQGPPQGFGVRPPQQFPMPPQQFGQRPMVPPPPGPMMRGPPSGP 241
           P       PP +    P  P        P    +PP           P       PP  P
Sbjct: 179 PASASPSDPPSSSPGVPSFPSPPEDPSSPSDSSLPP----------APSSFQSDTPPPSP 228

Query: 242 PRPGMPNAPPPRPGMPPPPGAPVFRPGMPPPPPNAQQQQQNQQQQ 286
             P  P+ PP     PPPP   V         P            
Sbjct: 229 ESPTNPSPPPGPAAPPPPPVQQVPPL--STAKPTPPSASATPAPI 271

Vta1 (VPS20-associated protein 1) is a positive regulator of Vps4. Vps4 is an ATPase that is required in the multivesicular body (MVB) sorting pathway to dissociate the endosomal sorting complex required for transport (ESCRT). Vta1 promotes correct assembly of Vps4 and stimulates its ATPase activity through its conserved Vta1/SBP1/LIP5 region. Length = 315

>gnl|CDD|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau; Validated

 Score = 47.3 bits (113), Expect = 5e-06
 Identities = 30/165 (18%), Positives = 37/165 (22%)

Query: 78  GEEVISMTVEGPPPPEESRAKAVSASAVAGPGIGRAAGRGVPAAPLVQAQPGLAGPVRGV 137
            E   +       P    +  AV  ++  G G    AG   PAAP     P       G 
Sbjct: 637 AEASAAPAPGVAAPEHHPKHVAVPDASDGGDGWPAKAGGAAPAAPPPAPAPAAPAAPAGA 696

Query: 138 GGPAPGMMQPQISRPPIPQLSAPPMTYPATSGGPPVIRPPGQMPPPVYPGQGPPMARGPP 197
               P                A      A     P       +P P  P   P  A  P 
Sbjct: 697 APAQPAPAPAATPPAGQADDPAAQPPQAAQGASAPSPAADDPVPLPPEPDDPPDPAGAPA 756

Query: 198 PQGPPQGFGVRPPQQFPMPPQQFGQRPMVPPPPGPMMRGPPSGPP 242
              PP             PP    +   +     P M        
Sbjct: 757 QPPPPPAPAPAAAPAAAPPPSPPSEEEEMAEDDAPSMDDEDRRDA 801

Length = 824

>gnl|CDD|237605 PRK14086, dnaA, chromosomal replication initiation protein; Provisional

 Score = 47.1 bits (112), Expect = 5e-06
 Identities = 46/195 (23%), Positives = 53/195 (27%), Gaps = 20/195 (10%)

Query: 86  VEGPPPPEESRAKAVSASAVAGPGIGRAAGRGVPAAPLVQAQPGLAGPVRGVGGPAPGMM 145
            E  PPP         A   + P + R   R        +A     G  R    P     
Sbjct: 93  GEPAPPPPH-------ARRTSEPELPRPGRRPYEGYGGPRADDRPPGLPRQDQLPTARPA 145

Query: 146 QPQISRPPIP-QLSAPPMTYP--ATSGGPPVIRPPGQMPPPVYPGQGPPMARGPPPQGPP 202
            P   + P P         Y       G P   P      P          R P   G P
Sbjct: 146 YPAYQQRPEPGAWPRAADDYGWQQQRLGFP---PRAPYASPASYAPEQERDREPYDAGRP 202

Query: 203 QGFGVRPPQQFP-----MPPQQFGQRPMVPPPPGPMMRGPPSGPPRPGMP--NAPPPRPG 255
           +    R     P      P +    RP  PP  G + RG P  P R   P     P  PG
Sbjct: 203 EYDQRRRDYDHPRPDWDRPRRDRTDRPEPPPGAGHVHRGGPGPPERDDAPVVPIRPSAPG 262

Query: 256 MPPPPGAPVFRPGMP 270
                 AP   PG P
Sbjct: 263 PLAAQPAPAPGPGEP 277

Length = 617

>gnl|CDD|212485 cd01739, LSm11_M, Like-Sm protein 11, middle domain

 Score = 42.2 bits (100), Expect = 8e-06
 Identities = 14/58 (24%), Positives = 24/58 (41%), Gaps = 6/58 (10%)

Query: 9  MLQFINYRMRVTIQDGRQ------LVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNN 60
          + +++  R RV +   +         G  +AFD+H NL L D +E       K  +  
Sbjct: 1  LHRWMRDRTRVKVYIRKAKGIRGSCEGYLVAFDKHWNLALVDVDETWTRRKYKYGEQA 58

The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm11 is an SmD2-like subunit which binds U7 snRNA along with LSm10 and five other Sm subunits to form a 7-membered ring structure. LSm11 and the U7 snRNP of which it is a part are thought to play an important role in histone mRNA 3' processing. Length = 63

>gnl|CDD|179104 PRK00737, PRK00737, small nuclear ribonucleoprotein; Provisional

 Score = 42.3 bits (100), Expect = 1e-05
 Identities = 21/64 (32%), Positives = 33/64 (51%), Gaps = 14/64 (21%)

Query: 19 VTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRG 78
          V ++ GR+  G+   +D HMNLVL + EE               ++ E  R LG V++RG
Sbjct: 19 VRLKGGREFRGELQGYDIHMNLVLDNAEEI--------------QDGEVVRKLGKVVIRG 64

Query: 79 EEVI 82
          + V+
Sbjct: 65 DNVV 68

Length = 72

>gnl|CDD|237874 PRK14971, PRK14971, DNA polymerase III subunits gamma and tau; Provisional

 Score = 45.2 bits (107), Expect = 2e-05
 Identities = 21/113 (18%), Positives = 28/113 (24%), Gaps = 15/113 (13%)

Query: 186 PGQGPPMARGPPPQGPPQGFGVRPPQQFPMPPQQFGQRPMVPPPPGPMMRGPPSGPPRPG 245
            G+GP     P    P        P           Q      P  P     P+G P   
Sbjct: 371 GGRGPKQHIKPVFTQPAAA---PQPSAAAAASPSPSQSSAAAQPSAPQSATQPAGTPPTV 427

Query: 246 MPNAPPPRPGMPPPPGAPVFRPGMPPPP------------PNAQQQQQNQQQQ 286
             + P   P  PP       RP                  P+  +  Q + +Q
Sbjct: 428 SVDPPAAVPVNPPSTAPQAVRPAQFKEEKKIPVSKVSSLGPSTLRPIQEKAEQ 480

Length = 614

>gnl|CDD|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1, 2, 3, 4 family

 Score = 45.2 bits (107), Expect = 3e-05
 Identities = 22/107 (20%), Positives = 33/107 (30%), Gaps = 6/107 (5%)

Query: 151 RPPIPQLSAPPMTYPATSGGPPVIRPPGQMPPPVYP---GQGPPMARGPPPQGPPQGFGV 207
           +P + QL           G PP      Q      P    +   M     P GP +  G+
Sbjct: 379 QPRMRQLPMG-SPMGGAMGQPPYYGQGPQQQFNGQPLGWPRMSMMPTPMGPGGPLRPNGL 437

Query: 208 RPPQQFPMPPQQFGQRPMVPPPPGPMMRGPPSGPPRPGMPNAPPPRP 254
            P      P +    +     PP   +  PP+    P   + P P+ 
Sbjct: 438 APMNAVRAPSRN--AQNAAQKPPMQPVMYPPNYQSLPLSQDLPQPQS 482

These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis (GP:11610605_PABP3 ), platelets (SP:Q13310_PABP4 ), broadly expressed (SP:P11940_PABP1) and of unknown tissue range (SP:Q15097_PABP2). Length = 562

>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional

 Score = 44.9 bits (106), Expect = 4e-05
 Identities = 41/176 (23%), Positives = 51/176 (28%), Gaps = 13/176 (7%)

Query: 118  VPAAPLVQAQPGLAGPVRGVGGPAPGMMQPQISRPPIPQLSAPPMTYPATSGGPPVIRPP 177
            +P A    A      P R    P+   +  +  RP  P  SA P       G P    PP
Sbjct: 2555 LPPAAPPAAPDRSVPPPRPAPRPSEPAVTSRARRPDAPPQSARPRAPVDDRGDPRGPAPP 2614

Query: 178  GQMPPPVYPGQGPPMARGPPPQGPPQGFGVRPP-----QQFPMPPQQFGQRPMVPPPPGP 232
              +PP  +    PP +  P    P        P     +  P P +    R         
Sbjct: 2615 SPLPPDTHAPDPPPPSPSPAANEPDPHPPPTVPPPERPRDDPAPGRVSRPRRARRLGRAA 2674

Query: 233  MMRGPPSGPPRPGMPN--------APPPRPGMPPPPGAPVFRPGMPPPPPNAQQQQ 280
                PP  P R             A PP P   P P         P PP  A  +Q
Sbjct: 2675 QASSPPQRPRRRAARPTVGSLTSLADPPPPPPTPEPAPHALVSATPLPPGPAAARQ 2730

Length = 3151

>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional

 Score = 44.5 bits (105), Expect = 5e-05
 Identities = 42/182 (23%), Positives = 52/182 (28%), Gaps = 15/182 (8%)

Query: 88   GPPPPEESRAKAVSASAVAGPGIGRAAGRGVPAAPLVQAQPGLAGPVRGVGGPAPGMMQP 147
            GP PP  S            P      G  V     V+ +P    P      PA    +P
Sbjct: 2826 GPLPPPTSAQPTAPPPPPGPPPPSLPLGGSVAPGGDVRRRPPSRSPAAKPAAPA----RP 2881

Query: 148  QISRPPIPQLSAPPMTYPATSGGPPVIRPPGQMPPPVYPGQGPPMARGPPPQGPPQGFGV 207
             + R   P +S    ++      P     P   PPP    Q PP  + P P  PP     
Sbjct: 2882 PVRRLARPAVSRSTESFALPPDQPERPPQPQAPPPPQPQPQPPPPPQ-PQPPPPPPPRPQ 2940

Query: 208  RPPQQFPMPPQQFGQRPMVPPP----------PGPMMRGPPSGPPRPGMPNAPPPRPGMP 257
             P      P         VP P            P  R P   P R    ++ PP  G  
Sbjct: 2941 PPLAPTTDPAGAGEPSGAVPQPWLGALVPGRVAVPRFRVPQPAPSREAPASSTPPLTGHS 3000

Query: 258  PP 259
              
Sbjct: 3001 LS 3002

Length = 3151

>gnl|CDD|212479 cd01732, LSm5, Like-Sm protein 5

 Score = 40.7 bits (96), Expect = 5e-05
 Identities = 22/77 (28%), Positives = 37/77 (48%), Gaps = 14/77 (18%)

Query: 13 INYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRT-L 71
          I  ++ + ++  ++ VG  + FD ++N+VL D  E+            T E R  + T L
Sbjct: 12 IGSKIWIIMKSDKEFVGTLLGFDDYVNMVLEDVTEY----------EITPEGR--KITKL 59

Query: 72 GLVLLRGEEVISMTVEG 88
            +LL G   I+M V G
Sbjct: 60 DQILLNGNN-IAMLVPG 75

The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a hetero-heptameric ring around the 3'-terminus uridylation tag of the gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA. LSm2-8 form the core of the snRNP particle that, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. LSm1-7 is involved in recognition of the 3' uridylation tag and recruitment of the decapping machinery. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Length = 76

>gnl|CDD|212473 cd01726, LSm6, Like-Sm protein 6

 Score = 39.8 bits (94), Expect = 6e-05
 Identities = 20/73 (27%), Positives = 29/73 (39%), Gaps = 16/73 (21%)

Query: 13 INYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLG 72
          I   + V +++G +  G     D +MNLVL D EE+       G+              G
Sbjct: 10 IGKPVVVKLKNGVEYRGVLACLDGYMNLVLEDTEEY-----VDGQL---------VAKYG 55

Query: 73 LVLLRGEEV--IS 83
             +RG  V  IS
Sbjct: 56 DAFIRGNNVLYIS 68

The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a hetero-heptameric ring around the 3'-terminus uridylation tag of the gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA. LSm2-8 form the core of the snRNP particle that, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. LSm1-7 is involved in recognition of the 3' uridylation tag and recruitment of the decapping machinery. LSm657 is believed to be an assembly intermediate for both the LSm1-7 and LSm2-8 rings. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Length = 68

>gnl|CDD|218621 pfam05518, Totivirus_coat, Totivirus coat protein

 Score = 44.0 bits (104), Expect = 7e-05
 Identities = 25/104 (24%), Positives = 29/104 (27%), Gaps = 7/104 (6%)

Query: 175 RPPGQMPPPVYPGQGPPMARGP--PPQGPPQGFGVRP-PQQFPMPPQQFGQRPMVPPPPG 231
              G+   P  PG  P         P    +G  VRP      +   Q   RP  PP  G
Sbjct: 649 NRGGEAGGPGVPGPVPVGMPAHTARPSRVARGDPVRPTAHHAALRAPQA-PRPGGPPGGG 707

Query: 232 PMMRGPPSGPPRPGMPNAP---PPRPGMPPPPGAPVFRPGMPPP 272
             +  PP  P   G           P  PP P  P         
Sbjct: 708 GGLPPPPDLPAAAGPAPCGSSLIASPTAPPEPEPPGAEQADGAE 751

Length = 753

>gnl|CDD|212469 cd01722, Sm_F, Sm protein F

 Score = 39.9 bits (94), Expect = 7e-05
 Identities = 17/65 (26%), Positives = 27/65 (41%), Gaps = 14/65 (21%)

Query: 13 INYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLG 72
              + V ++ G +  G  ++ D +MNL L + EE+       GK             LG
Sbjct: 10 TGKPVIVKLKWGMEYKGTLVSVDSYMNLQLANTEEY-----IDGKFTG---------NLG 55

Query: 73 LVLLR 77
           VL+R
Sbjct: 56 EVLIR 60

The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a hetero-heptameric ring around the Sm site of the 2,2,7-trimethyl guanosine (m3G) capped U1, U2, U4 and U5 snRNAs (Sm snRNAs) forming the core of the snRNP particle. The snRNP particle, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit F is capable of forming both homo- and hetero-heptamer ring structures. To form the hetero-heptamer, Sm subunit F initially binds subunits E and G to form a trimer which then assembles onto snRNA along with the D3/B and D1/D2 heterodimers. Length = 69

>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional

 Score = 43.8 bits (103), Expect = 9e-05
 Identities = 49/193 (25%), Positives = 56/193 (29%), Gaps = 18/193 (9%)

Query: 89   PPPPEESRAKAVSASAVAGPGIGRAAGRGVPAAPLVQAQPGLAGPVRGVGGPAPGMMQPQ 148
            PPPP  S A                  R  PA   V          R     +P    PQ
Sbjct: 2626 PPPPSPSPAANEPDPHPPPTVPPPERPRDDPAPGRVSRPRRARRLGRAAQASSP----PQ 2681

Query: 149  ISRPPIPQLSAPPMTYPATSGGPPVIRPPGQMPPPVYPGQGPPMARGPPPQGPPQGFGVR 208
              R      +A P     TS   P   PP   P P        ++  P P GP       
Sbjct: 2682 RPRRR----AARPTVGSLTSLADPPPPPPTPEPAPH-----ALVSATPLPPGPAAARQAS 2732

Query: 209  PPQQFPMPPQQFGQRPMVPPPPGPMMRGP-PSGPPRPGMPNAPP--PRPGMPPPPGAP-- 263
            P       P      P  P  P    R P  +GPP P  P AP   P   +  P  A   
Sbjct: 2733 PALPAAPAPPAVPAGPATPGGPARPARPPTTAGPPAPAPPAAPAAGPPRRLTRPAVASLS 2792

Query: 264  VFRPGMPPPPPNA 276
              R  +P P   A
Sbjct: 2793 ESRESLPSPWDPA 2805

Length = 3151

>gnl|CDD|237874 PRK14971, PRK14971, DNA polymerase III subunits gamma and tau; Provisional

 Score = 42.8 bits (101), Expect = 1e-04
 Identities = 19/143 (13%), Positives = 30/143 (20%), Gaps = 21/143 (14%)

Query: 148 QISRPPIPQLSAPPMTYPATSGGPPVIRPPGQMPPPVY--PGQGPPMARGPPPQGPPQGF 205
           Q+++       A     P     P   +P     P         P  +            
Sbjct: 358 QLAQLTQKGDDASGGRGPKQHIKPVFTQPAAAPQPSAAAAASPSPSQSSAAAQ------- 410

Query: 206 GVRPPQQFPMPPQQFGQRPMVPPPPGPMMRGPPS-GPPRPGMPNAPPPRPGMPPPPGAPV 264
              P               +   PP  +   PPS  P           +         PV
Sbjct: 411 ---PSAPQSATQPAGTPPTVSVDPPAAVPVNPPSTAPQAVRPAQFKEEKK-------IPV 460

Query: 265 FRPGM-PPPPPNAQQQQQNQQQQ 286
            +     P      Q++  Q   
Sbjct: 461 SKVSSLGPSTLRPIQEKAEQATG 483

Length = 614

>gnl|CDD|220392 pfam09770, PAT1, Topoisomerase II-associated protein PAT1

 Score = 42.1 bits (99), Expect = 2e-04
 Identities = 44/195 (22%), Positives = 56/195 (28%), Gaps = 29/195 (14%)

Query: 70  TLGLVLLRGEEVISMTVEGPPPPEESRAKAVSASAVAGPGIGRAAGRGVPAAPLVQAQPG 129
           T    +L  EEV +   +    P+  +           P       +G P  P    QP 
Sbjct: 148 TPAQKMLSLEEVEAQLQQRQQAPQLPQPPQQVLPQGMPPRQAAFPQQGPPEQPPGYPQPP 207

Query: 130 LAGPVRGVGG---PAPGMMQPQISRPPIPQLSAPPMTYPATSGG-----PPVIRPPGQMP 181
              P +       PAP     Q   PP      PP+  P   G      PP  +PP Q  
Sbjct: 208 QGHPEQVQPQQFLPAPSQAPAQPPLPPQLPQQPPPLQQPQFPGLSQQMPPPPPQPPQQQQ 267

Query: 182 PPVYP-GQGPPMARGPPPQGPPQG--------------------FGVRPPQQFPMPPQQF 220
            P  P  Q PP  +  P  G PQG                     G +   QF     Q 
Sbjct: 268 QPPQPQAQPPPQNQPTPHPGLPQGQNAPLPPPQQPQLLPLVQQPQGQQRGPQFREQLVQL 327

Query: 221 GQRPMVPPPPGPMMR 235
            Q+           R
Sbjct: 328 SQQQREALSQEEAKR 342

Members of this family are necessary for accurate chromosome transmission during cell division. Length = 804

>gnl|CDD|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau; Validated

 Score = 42.3 bits (100), Expect = 2e-04
 Identities = 21/120 (17%), Positives = 23/120 (19%), Gaps = 1/120 (0%)

Query: 161 PMTYPATSGGPPVIRPPGQMPPPVYPGQGPPMARGPPPQGPPQGFGVRPPQQFPMPPQQF 220
            +   A +            P           A    P           P   P  P   
Sbjct: 386 GVAGGAGAPAAAAPSAAAAAPAAAPAPAAAAPAAAAAPAPAAAPQPAPAPAPAP-APPSP 444

Query: 221 GQRPMVPPPPGPMMRGPPSGPPRPGMPNAPPPRPGMPPPPGAPVFRPGMPPPPPNAQQQQ 280
                    P P     PS  P P    AP P     P P A       P  P       
Sbjct: 445 AGNAPAGGAPSPPPAAAPSAQPAPAPAAAPEPTAAPAPAPPAAPAPAAAPAAPAAPAAPA 504

Length = 824

>gnl|CDD|237057 PRK12323, PRK12323, DNA polymerase III subunits gamma and tau; Provisional

 Score = 42.2 bits (99), Expect = 2e-04
 Identities = 22/123 (17%), Positives = 22/123 (17%), Gaps = 3/123 (2%)

Query: 159 APPMTYPATSGGPPVIRPPGQMPPPVYPGQGPPMARGPPPQGPPQGFGVRPPQQFPMPPQ 218
           A     P     P    P    P P  P   P  A                    P    
Sbjct: 375 ATAAAAPVAQPAPAAAAPAAAAPAPAAPPAAPAAAPAAAAAARAVAAAPARRSPAPEALA 434

Query: 219 QFGQRPMVPPPPGPMMRGPPSGPPRPGMPNAPPPRPGMPPPPGAPVFRPGMPPPPPNAQQ 278
              Q     P   P    P   P       A P   G  P   A    P    P      
Sbjct: 435 AARQASARGPGGAP---APAPAPAAAPAAAARPAAAGPRPVAAAAAAAPARAAPAAAPAP 491

Query: 279 QQQ 281
              
Sbjct: 492 ADD 494

Length = 700

>gnl|CDD|236669 PRK10263, PRK10263, DNA translocase FtsK; Provisional

 Score = 42.8 bits (100), Expect = 2e-04
 Identities = 39/187 (20%), Positives = 55/187 (29%), Gaps = 6/187 (3%)

Query: 91  PPEESRAKAVSASAVAGPGIGRAAGRGVPAAPLVQAQPGLA-GPVRGVGGPAPGMMQPQI 149
           P   + A   +  + A P         V +  +  AQP +A  PV G     P +     
Sbjct: 319 PVAVAAAATTATQSWAAPVEPVTQTPPVASVDVPPAQPTVAWQPVPGPQTGEPVIAPAPE 378

Query: 150 SRPPIPQLSAPPMTYPATSGGPPVIRPPGQMPPPVYPGQGPPMARGPP-----PQGPPQG 204
             P   Q + P + Y      P   + P   P    P Q P  A  P      P   P  
Sbjct: 379 GYPQQSQYAQPAVQYNEPLQQPVQPQQPYYAPAAEQPAQQPYYAPAPEQPAQQPYYAPAP 438

Query: 205 FGVRPPQQFPMPPQQFGQRPMVPPPPGPMMRGPPSGPPRPGMPNAPPPRPGMPPPPGAPV 264
                   +    QQ    P          + P +  P    P     +P + P P    
Sbjct: 439 EQPVAGNAWQAEEQQSTFAPQSTYQTEQTYQQPAAQEPLYQQPQPVEQQPVVEPEPVVEE 498

Query: 265 FRPGMPP 271
            +P  PP
Sbjct: 499 TKPARPP 505

Length = 1355

>gnl|CDD|236382 PRK09111, PRK09111, DNA polymerase III subunits gamma and tau; Validated

 Score = 41.8 bits (99), Expect = 2e-04
 Identities = 14/83 (16%), Positives = 16/83 (19%), Gaps = 11/83 (13%)

Query: 179 QMPPPVYPGQGPPMARGPPPQGPPQGFGVRPPQQFPMPPQQFGQRPMVPPPPGPMMRGPP 238
           + PP    G G P   G  P  P                            P   +   P
Sbjct: 389 EGPPSPGGGGGGPPGGGGAPGAPA-----------AAAAPGAAAAAPAAGGPAAALAAVP 437

Query: 239 SGPPRPGMPNAPPPRPGMPPPPG 261
                   P AP   P       
Sbjct: 438 DAAAAAAAPPAPAAAPQPAVRLN 460

Length = 598

>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional

 Score = 41.8 bits (98), Expect = 3e-04
 Identities = 46/206 (22%), Positives = 54/206 (26%), Gaps = 19/206 (9%)

Query: 90   PPPEESRAKAVSASAVAGPGIGRAAGRGVPAAPLVQAQPGLAGPVRGVGGPAPGMMQPQI 149
            P      ++A    A       RA        P   A P    P      P P    P  
Sbjct: 2577 PSEPAVTSRARRPDAPPQSARPRAPV-DDRGDPRGPAPPSPLPPDTHAPDPPPPSPSPAA 2635

Query: 150  SRPPIPQ-LSAPPMTYPATSGGPPVIRPP------GQMPPPVYPGQGPPMARGPPPQGPP 202
            + P      + PP   P     P  +  P      G+      P Q P      P  G  
Sbjct: 2636 NEPDPHPPPTVPPPERPRDDPAPGRVSRPRRARRLGRAAQASSPPQRPRRRAARPTVGSL 2695

Query: 203  QGFGVRPPQQFPMPPQQFGQRPMVPPPPGPMMRG-----PPSGPPRPGMPNAP-----PP 252
                  PP      P         P PPGP          P+ P  P +P  P     P 
Sbjct: 2696 TSLADPPPPPPTPEPAPHALVSATPLPPGPAAARQASPALPAAPAPPAVPAGPATPGGPA 2755

Query: 253  RPGMPPPPGAPVFRPGMPPPPPNAQQ 278
            RP  PP    P   P  P  P     
Sbjct: 2756 RPARPPTTAGPP-APAPPAAPAAGPP 2780

Length = 3151

>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional

 Score = 41.8 bits (98), Expect = 3e-04
 Identities = 44/189 (23%), Positives = 57/189 (30%), Gaps = 20/189 (10%)

Query: 112  RAAGRGVPAAPLVQAQPGLAGPVRGVGGPAPGMMQPQISRPPIPQLSAPPMTYPATSGGP 171
               G   P AP+ +       P      P PG   P     P       P   P    G 
Sbjct: 2468 LLLGELFPGAPVYRRPAEARFPFAAGAAPDPGGGGPPDPDAPPAPSRLAPAILPDEPVGE 2527

Query: 172  PV-------IRPPGQMPPPVYPGQGPPMARGPPPQGPPQGFGVRPPQQFPMPP----QQF 220
            PV       IR   ++         PP+    PP  P +   V PP+  P P        
Sbjct: 2528 PVHPRMLTWIRGLEELASDDAGDPPPPLPPAAPPAAPDRS--VPPPRPAPRPSEPAVTSR 2585

Query: 221  GQRPMVPP-------PPGPMMRGPPSGPPRPGMPNAPPPRPGMPPPPGAPVFRPGMPPPP 273
             +RP  PP       P           PP P  P+   P P  P P  A       PPP 
Sbjct: 2586 ARRPDAPPQSARPRAPVDDRGDPRGPAPPSPLPPDTHAPDPPPPSPSPAANEPDPHPPPT 2645

Query: 274  PNAQQQQQN 282
                ++ ++
Sbjct: 2646 VPPPERPRD 2654

Length = 3151

>gnl|CDD|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau; Validated

 Score = 41.9 bits (99), Expect = 3e-04
 Identities = 24/118 (20%), Positives = 28/118 (23%), Gaps = 3/118 (2%)

Query: 87  EGPPPPEESRAKAVSASAVAGPGIGRAAGRGVPAAPLVQAQPGLAGPVRGVGGPAPGMMQ 146
            G P      A A + +A   P     A    PA     A P  A        P      
Sbjct: 391 AGAPAAAAPSAAAAAPAAAPAPAAAAPAAAAAPAPA---AAPQPAPAPAPAPAPPSPAGN 447

Query: 147 PQISRPPIPQLSAPPMTYPATSGGPPVIRPPGQMPPPVYPGQGPPMARGPPPQGPPQG 204
                 P P  +A P   PA +            P P            P     P G
Sbjct: 448 APAGGAPSPPPAAAPSAQPAPAPAAAPEPTAAPAPAPPAAPAPAAAPAAPAAPAAPAG 505

Length = 824

>gnl|CDD|237864 PRK14950, PRK14950, DNA polymerase III subunits gamma and tau; Provisional

 Score = 41.7 bits (98), Expect = 3e-04
 Identities = 27/101 (26%), Positives = 30/101 (29%), Gaps = 13/101 (12%)

Query: 181 PPPVYPGQGPPMARGPPPQGPPQGFGVRPPQQFPMPPQQFGQRPMVPPPPGPMMRGPPSG 240
           P P  P    P A  P P        VRP       P+      + P  P      PP  
Sbjct: 362 PVPA-PQPAKPTAAAPSP--------VRPTPAPSTRPKAAAAANIPPKEPVRETATPPPV 412

Query: 241 PPRPGMPNAPPPRPGMPPPPGA----PVFRPGMPPPPPNAQ 277
           PPRP  P  P      P    A           PP PP  +
Sbjct: 413 PPRPVAPPVPHTPESAPKLTRAAIPVDEKPKYTPPAPPKEE 453

Length = 585

>gnl|CDD|235904 PRK06995, flhF, flagellar biosynthesis regulator FlhF; Validated

 Score = 41.5 bits (98), Expect = 3e-04
 Identities = 16/120 (13%), Positives = 23/120 (19%), Gaps = 11/120 (9%)

Query: 165 PATSGGPPVIRPPGQMPPPVYPGQGPPMARGPPPQGPPQGFGVRPPQQFPMPPQQFGQRP 224
           PA +       PP   P  V     P     P      +    R   Q           P
Sbjct: 54  PAAAAPAAAQPPPAAAPAAVSRPAAPAAEPAPWLVEHAK----RLTAQR-EQLVARAAAP 108

Query: 225 MVPPPPGPMMRGPPSGPPRPGMPNAPPPRPGMPPPPGAPVFRPGMPPPPPNAQQQQQNQQ 284
             P          P+ P           R             P           + + ++
Sbjct: 109 AAPEA------QAPAAPAERAAAENAARRLARAAAAAPRPRVPADAAAAVADAVKARIER 162

Length = 484

>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional

 Score = 41.5 bits (97), Expect = 4e-04
 Identities = 42/197 (21%), Positives = 54/197 (27%), Gaps = 11/197 (5%)

Query: 89   PPPPEESRAKAVSASAVAGPGIGRAAGRGV-----PAAPLVQAQPGLAGPVRGVGGPAPG 143
              PP E      +   V+ P   R  GR       P  P  +A     G +  +  P P 
Sbjct: 2645 TVPPPERPRDDPAPGRVSRPRRARRLGRAAQASSPPQRPRRRAARPTVGSLTSLADPPPP 2704

Query: 144  MMQPQISRPP-IPQLSAPPMTYPATSGGPPVIRPPGQMPPPVYPGQGPPMARGPPPQGPP 202
               P+ +    +     PP    A    P +   P     P  P      AR   P    
Sbjct: 2705 PPTPEPAPHALVSATPLPPGPAAARQASPALPAAPAPPAVPAGPATPGGPARPARPPTTA 2764

Query: 203  QGFGVRPPQQFPMPPQQFGQRPMVPPPPGPMMRGPPSGPPRPGMPNAPPPRPGMPPPPGA 262
                  PP      P        +  P    +       P P  P  PP     P     
Sbjct: 2765 GPPAPAPPAAPAAGPP-----RRLTRPAVASLSESRESLPSPWDPADPPAAVLAPAAALP 2819

Query: 263  PVFRPGMPPPPPNAQQQ 279
            P   P  P PPP + Q 
Sbjct: 2820 PAASPAGPLPPPTSAQP 2836

Length = 3151

>gnl|CDD|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau; Validated

 Score = 41.1 bits (97), Expect = 5e-04
 Identities = 20/109 (18%), Positives = 20/109 (18%), Gaps = 1/109 (0%)

Query: 175 RPPGQMPPPVYPGQGPPMARGPPPQGPPQGFGVRPPQQFPMPPQQFGQRPMVPPPPGPMM 234
             P    P                               P P       P   P      
Sbjct: 392 GAPAAAAPSAAAAAPAAAPAPAAAAPAAAAAPAPAAAPQPAPAPAPAPAP-PSPAGNAPA 450

Query: 235 RGPPSGPPRPGMPNAPPPRPGMPPPPGAPVFRPGMPPPPPNAQQQQQNQ 283
            G PS PP       P P P   P P A         P P A       
Sbjct: 451 GGAPSPPPAAAPSAQPAPAPAAAPEPTAAPAPAPPAAPAPAAAPAAPAA 499

Length = 824

>gnl|CDD|237865 PRK14951, PRK14951, DNA polymerase III subunits gamma and tau; Provisional

 Score = 40.9 bits (96), Expect = 5e-04
 Identities = 25/115 (21%), Positives = 35/115 (30%), Gaps = 3/115 (2%)

Query: 89  PPPPEESRAKAVSASAVAGPGIGRAAGRGVPAAPLVQAQPGLAGPVRGVGGPAPGMMQPQ 148
            P  +++ A+  +A+  A P    AA     AAP   A    A P      P      P 
Sbjct: 374 APAEKKTPARPEAAAPAAAPVAQAAAAPAPAAAPAAAASAPAAPPAAAPPAPVA---APA 430

Query: 149 ISRPPIPQLSAPPMTYPATSGGPPVIRPPGQMPPPVYPGQGPPMARGPPPQGPPQ 203
            + P     +AP     A +           +P  V P      A   P   P  
Sbjct: 431 AAAPAAAPAAAPAAVALAPAPPAQAAPETVAIPVRVAPEPAVASAAPAPAAAPAA 485

Length = 618

>gnl|CDD|237871 PRK14965, PRK14965, DNA polymerase III subunits gamma and tau; Provisional

 Score = 40.9 bits (96), Expect = 5e-04
 Identities = 20/88 (22%), Positives = 22/88 (25%), Gaps = 19/88 (21%)

Query: 168 SGGPPVIRPPGQMPPPVYPGQGPPMARGPPPQGPPQGFGVRPPQQFPMPPQQFGQRPMVP 227
            G P         P P  P   PP A  PP                  P +    RP  P
Sbjct: 379 RGAPAPPSAAWGAPTPAAPAA-PPPAAAPPVPPAA-------------PARPAAARP-AP 423

Query: 228 PPPGPMMRGPPSGPPRPGMPNAPPPRPG 255
            P  P      + PP      A     G
Sbjct: 424 APAPP----AAAAPPARSADPAAAASAG 447

Length = 576

>gnl|CDD|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau; Validated

 Score = 40.7 bits (96), Expect = 6e-04
 Identities = 22/121 (18%), Positives = 25/121 (20%), Gaps = 6/121 (4%)

Query: 99  AVSASAVAGPGIGRAAGRGVPAAPLVQAQPGLAGPVRGVGGPAPGMMQPQISRPPIPQLS 158
              A     P     +      A    A    A        PAP         P  P  +
Sbjct: 385 LGVAGGAGAPAAAAPSAAAAAPAA---APAPAAAAPAAAAAPAPAAAPQPAPAPA-PAPA 440

Query: 159 APPMTYPATSGGPPVIRPPGQMPPPVYPGQGPPMARGPPPQGPPQGFGVRPPQQFPMPPQ 218
            P     A +GG P   P         P           P   P       P   P  P 
Sbjct: 441 PPSPAGNAPAGGAPSPPPAAAPSAQPAPAPAAAPEPTAAPAPAPP--AAPAPAAAPAAPA 498

Query: 219 Q 219
            
Sbjct: 499 A 499

Length = 824

>gnl|CDD|237865 PRK14951, PRK14951, DNA polymerase III subunits gamma and tau; Provisional

 Score = 40.9 bits (96), Expect = 6e-04
 Identities = 19/135 (14%), Positives = 27/135 (20%), Gaps = 6/135 (4%)

Query: 108 PGIGRAAGRGVPAAPLVQAQPGLAGPVRGVGGPAPGMMQPQISRPPIPQLSAPPMTYPAT 167
           P     A          + +            P                 ++ P   PA 
Sbjct: 366 PAAAAEAAAPAEKKTPARPEAAAPAAA-----PVAQAAAAPAPAAAPAAAASAPAAPPAA 420

Query: 168 SGGPPVIRPPGQMPPPVYPGQGPPMARGPPPQGPPQGFGVRPPQQF-PMPPQQFGQRPMV 226
           +   PV  P    P          +A  P P        V  P +  P P          
Sbjct: 421 APPAPVAAPAAAAPAAAPAAAPAAVALAPAPPAQAAPETVAIPVRVAPEPAVASAAPAPA 480

Query: 227 PPPPGPMMRGPPSGP 241
             P    +     G 
Sbjct: 481 AAPAAARLTPTEEGD 495

Length = 618

>gnl|CDD|218191 pfam04652, DUF605, Vta1 like

 Score = 40.1 bits (94), Expect = 7e-04
 Identities = 22/100 (22%), Positives = 27/100 (27%), Gaps = 1/100 (1%)

Query: 156 QLSAPPMTYPATSGGPPVIRPPGQMPPPVYPGQGPPMARGPPPQGPPQGFGVRPPQQFPM 215
             SA P   P++S G P    P + P        PP         PP           P 
Sbjct: 179 PASASPSDPPSSSPGVPSFPSPPEDPSSPSDSSLPPAPSSFQSDTPPPSPESPTNPSPPP 238

Query: 216 PPQQFGQRPMVPPPPGPMMR-GPPSGPPRPGMPNAPPPRP 254
            P      P+   PP    +  PPS    P          
Sbjct: 239 GPAAPPPPPVQQVPPLSTAKPTPPSASATPAPIGGITLDD 278

Vta1 (VPS20-associated protein 1) is a positive regulator of Vps4. Vps4 is an ATPase that is required in the multivesicular body (MVB) sorting pathway to dissociate the endosomal sorting complex required for transport (ESCRT). Vta1 promotes correct assembly of Vps4 and stimulates its ATPase activity through its conserved Vta1/SBP1/LIP5 region. Length = 315

>gnl|CDD|237057 PRK12323, PRK12323, DNA polymerase III subunits gamma and tau; Provisional

 Score = 40.2 bits (94), Expect = 8e-04
 Identities = 27/120 (22%), Positives = 31/120 (25%), Gaps = 9/120 (7%)

Query: 165 PATSGGPPVIRPPGQMPPPVYPGQGPPMARGPPPQGPPQGFGVRPPQQFPMPPQQFGQRP 224
           PAT+   PV +P         P    P A  P P  PP      P               
Sbjct: 374 PATAAAAPVAQPA--------PAAAAPAAAAPAPAAPPAAPAAAPAAAAAARAVAAAPAR 425

Query: 225 MVPPPPGPMMRGPPSGPPRPGMPNAPPPRPGMPPPPGAPVFRPGMPPPPPNAQQQQQNQQ 284
              P P  +     +    PG   AP P P   P   A     G  P    A        
Sbjct: 426 R-SPAPEALAAARQASARGPGGAPAPAPAPAAAPAAAARPAAAGPRPVAAAAAAAPARAA 484

Length = 700

>gnl|CDD|237057 PRK12323, PRK12323, DNA polymerase III subunits gamma and tau; Provisional

 Score = 40.2 bits (94), Expect = 9e-04
 Identities = 36/180 (20%), Positives = 43/180 (23%), Gaps = 11/180 (6%)

Query: 107 GPGIGRAAGRGVPAAPLVQAQPGLAGPVRGVGGPAPGMMQPQISRPPIPQLSAPPMTYPA 166
           G   G A      AAP+ Q  P  A P      PA     P  + P     +      PA
Sbjct: 366 GQSGGGAGPATAAAAPVAQPAPAAAAPAAAAPAPAAPPAAPAAA-PAAAAAARAVAAAPA 424

Query: 167 TSGGPPVIRPPGQMPPPVYPGQGPPMARGPPPQGPPQGFGVRPPQQFPMPPQQFGQRPMV 226
                P      +      PG  P  A  P           RP    P P          
Sbjct: 425 RRSPAPEALAAARQASARGPGGAPAPAPAPAAAPAAA---ARPAAAGPRPVAAAAAAAPA 481

Query: 227 PPPPGPMMRGPPSGPP----RPGMPNAPPPRPGMPPPPG---APVFRPGMPPPPPNAQQQ 279
              P          PP     P    +P P      P G     +  P    P    +  
Sbjct: 482 RAAPAAAPAPADDDPPPWEELPPEFASPAPAQPDAAPAGWVAESIPDPATADPDDAFETL 541

Length = 700

>gnl|CDD|218191 pfam04652, DUF605, Vta1 like

 Score = 39.3 bits (92), Expect = 0.001
 Identities = 23/106 (21%), Positives = 26/106 (24%), Gaps = 9/106 (8%)

Query: 190 PPMARGPPPQGPPQGFGVRPPQQFPMPPQQFGQRPMVPPPPGPMMRGPPSGPPRPG---- 245
            P    P  +                P +        P  P     G PS P  P     
Sbjct: 147 DPNPGPPLDEEDEDADVATTNSDNSFPGEDADPASASPSDPPSSSPGVPSFPSPPEDPSS 206

Query: 246 -----MPNAPPPRPGMPPPPGAPVFRPGMPPPPPNAQQQQQNQQQQ 286
                +P AP       PPP         PPP P A      QQ  
Sbjct: 207 PSDSSLPPAPSSFQSDTPPPSPESPTNPSPPPGPAAPPPPPVQQVP 252

Vta1 (VPS20-associated protein 1) is a positive regulator of Vps4. Vps4 is an ATPase that is required in the multivesicular body (MVB) sorting pathway to dissociate the endosomal sorting complex required for transport (ESCRT). Vta1 promotes correct assembly of Vps4 and stimulates its ATPase activity through its conserved Vta1/SBP1/LIP5 region. Length = 315

>gnl|CDD|237874 PRK14971, PRK14971, DNA polymerase III subunits gamma and tau; Provisional

 Score = 39.8 bits (93), Expect = 0.001
 Identities = 26/136 (19%), Positives = 38/136 (27%), Gaps = 8/136 (5%)

Query: 85  TVEGPPPPEESRAKAVSASAVAGPGIGRAAGRGVPAAPLVQAQPGLAGPVRGVGGPAPGM 144
              G   P++      +  A A      AA    P+     AQP          G  P +
Sbjct: 368 DASGGRGPKQHIKPVFTQPAAAPQPSAAAAASPSPSQSSAAAQPSAPQSATQPAGTPPTV 427

Query: 145 MQPQISRPPIPQLSAPPMTYPATSGGPPVIRPPGQMPPPVYPGQGPPMARGPPPQGPPQG 204
                  PP      PP T P  +  P   +   ++P       GP   R   P      
Sbjct: 428 SVD----PPAAVPVNPPSTAP-QAVRPAQFKEEKKIPVSKVSSLGPSTLR---PIQEKAE 479

Query: 205 FGVRPPQQFPMPPQQF 220
                 ++ P   Q+ 
Sbjct: 480 QATGNIKEAPTGTQKE 495

Length = 614

>gnl|CDD|235124 PRK03427, PRK03427, cell division protein ZipA; Provisional

 Score = 39.2 bits (92), Expect = 0.001
 Identities = 24/124 (19%), Positives = 33/124 (26%)

Query: 158 SAPPMTYPATSGGPPVIRPPGQMPPPVYPGQGPPMARGPPPQGPPQGFGVRPPQQFPMPP 217
                   A         P  Q  PP    Q     + PP    P     RP Q  P P 
Sbjct: 70  RVNHAPANAQEHEAARPSPQHQYQPPYASAQPRQPVQQPPEAQVPPQHAPRPAQPAPQPV 129

Query: 218 QQFGQRPMVPPPPGPMMRGPPSGPPRPGMPNAPPPRPGMPPPPGAPVFRPGMPPPPPNAQ 277
           QQ   +P    P    +    +  P+P      P +    P       +P     P    
Sbjct: 130 QQPAYQPQPEQPLQQPVSPQVAPAPQPVHSAPQPAQQAFQPAEPVAAPQPEPVAEPAPVM 189

Query: 278 QQQQ 281
            + +
Sbjct: 190 DKPK 193

Length = 333

>gnl|CDD|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau; Validated

 Score = 39.6 bits (93), Expect = 0.002
 Identities = 24/138 (17%), Positives = 29/138 (21%), Gaps = 8/138 (5%)

Query: 116 RGVPAAPLVQAQPGLAGPVRGVGGPAPGMMQPQISRPPIPQLSAPPMTYPATSGGPPVIR 175
           R   A                    AP    P  + P      AP    P  +  P    
Sbjct: 384 RLGVAGGAGAPAAAAPSAAAAAPAAAPA---PAAAAPAAAAAPAPA-AAPQPAPAPAPAP 439

Query: 176 PPGQMPPPVYPGQGPPMARGPPPQGPPQGFGVRPPQQFPMPPQQFGQRPMVPPPPGPMMR 235
            P         G  P       P   P       P+    P       P   P P     
Sbjct: 440 APPSPAGNAPAGGAPSPPPAAAPSAQPAPAPAAAPEPTAAPAPA----PPAAPAPAAAPA 495

Query: 236 GPPSGPPRPGMPNAPPPR 253
            P +     G  +A   R
Sbjct: 496 APAAPAAPAGADDAATLR 513

Length = 824

>gnl|CDD|237057 PRK12323, PRK12323, DNA polymerase III subunits gamma and tau; Provisional

 Score = 39.5 bits (92), Expect = 0.002
 Identities = 33/165 (20%), Positives = 41/165 (24%), Gaps = 12/165 (7%)

Query: 112 RAAGRGVPAAPLVQAQPGLAGPVRGVGGPAPGMMQPQISRPPIPQLSAPPMTYPATSGGP 171
           R    G  A P   A   +A P      PA        +  P    +AP     A +   
Sbjct: 364 RPGQSGGGAGPATAAAAPVAQPAPAAAAPAA------AAPAPAAPPAAPAAAPAAAAAAR 417

Query: 172 PVIRPPGQMPPPVYPGQGPPMARGPPPQGPPQGFGVRPPQQFPMPPQQFGQRPMVPPPPG 231
            V   P +  P          AR    +GP    G   P   P        RP    P  
Sbjct: 418 AVAAAPARRSPAPEA---LAAARQASARGPG---GAPAPAPAPAAAPAAAARPAAAGPRP 471

Query: 232 PMMRGPPSGPPRPGMPNAPPPRPGMPPPPGAPVFRPGMPPPPPNA 276
                  +           P     PP    P       P  P+A
Sbjct: 472 VAAAAAAAPARAAPAAAPAPADDDPPPWEELPPEFASPAPAQPDA 516

Length = 700

>gnl|CDD|237605 PRK14086, dnaA, chromosomal replication initiation protein; Provisional

 Score = 39.0 bits (91), Expect = 0.002
 Identities = 26/144 (18%), Positives = 34/144 (23%), Gaps = 13/144 (9%)

Query: 140 PAPGMMQPQISRPPIPQLSAPPMTYPATSGGPPVIRPPGQMPPPVYPGQGPPMARGPPPQ 199
             P     + S P +P        Y    G     RPPG       P   P      P  
Sbjct: 96  APPPPHARRTSEPELP--RPGRRPYEGYGGPRADDRPPGLPRQDQLPTARP----AYPAY 149

Query: 200 GPPQGFGVRPPQQFPMPPQQFGQRPMVPPPPGPMMRGPPSGPPRPGMPNAPPPRPGMP-- 257
                 G  P        Q   Q+ +  PP  P     P+        +  P   G P  
Sbjct: 150 QQRPEPGAWPRAADDYGWQ---QQRLGFPPRAPY--ASPASYAPEQERDREPYDAGRPEY 204

Query: 258 PPPGAPVFRPGMPPPPPNAQQQQQ 281
                    P      P   +  +
Sbjct: 205 DQRRRDYDHPRPDWDRPRRDRTDR 228

Length = 617

>gnl|CDD|218621 pfam05518, Totivirus_coat, Totivirus coat protein

 Score = 39.0 bits (91), Expect = 0.002
 Identities = 22/127 (17%), Positives = 25/127 (19%), Gaps = 12/127 (9%)

Query: 86  VEGPPPPEESRAKAVSASAVAGPGIGRAAGRGVPAAPLVQAQPGLAGPVRGVGGPAPGMM 145
           V     P     +   A     PG          A P   A+          G P     
Sbjct: 638 VFKTALPRPDYNRGGEAGGPGVPGPVPVGMPAHTARPSRVAR----------GDPVRPTA 687

Query: 146 QPQISRPPIPQLSAPPMTYPATSGGPPVIRPPGQMPPPVYPGQGPPMARGPPPQGPPQGF 205
                    PQ   P        G PP    P    P             PP   PP   
Sbjct: 688 HHA--ALRAPQAPRPGGPPGGGGGLPPPPDLPAAAGPAPCGSSLIASPTAPPEPEPPGAE 745

Query: 206 GVRPPQQ 212
                + 
Sbjct: 746 QADGAEN 752

Length = 753

>gnl|CDD|236669 PRK10263, PRK10263, DNA translocase FtsK; Provisional

 Score = 39.3 bits (91), Expect = 0.002
 Identities = 29/99 (29%), Positives = 35/99 (35%), Gaps = 2/99 (2%)

Query: 182 PPVYPGQGPPMARGPPPQGPPQGFGVRPPQQFPMPPQQFGQRPMVPPPPGPMMRGPPSGP 241
           P V P Q P     P  Q       V P  Q+  P Q    +P    P  P+   P    
Sbjct: 747 PIVEPVQQPQQPVAPQQQYQQPQQPVAPQPQYQQPQQPVAPQPQYQQPQQPVAPQPQYQQ 806

Query: 242 PRPGMPNAPPPRPGMPPPPGAPVFRPGMPPPPPNAQQQQ 280
           P+   P AP P+   P  P AP  +   P  P   Q Q 
Sbjct: 807 PQ--QPVAPQPQYQQPQQPVAPQPQYQQPQQPVAPQPQD 843

Length = 1355

>gnl|CDD|236382 PRK09111, PRK09111, DNA polymerase III subunits gamma and tau; Validated

 Score = 39.1 bits (92), Expect = 0.002
 Identities = 13/67 (19%), Positives = 16/67 (23%)

Query: 211 QQFPMPPQQFGQRPMVPPPPGPMMRGPPSGPPRPGMPNAPPPRPGMPPPPGAPVFRPGMP 270
           Q+ P  P   G  P              +       P A  P   +   P A       P
Sbjct: 388 QEGPPSPGGGGGGPPGGGGAPGAPAAAAAPGAAAAAPAAGGPAAALAAVPDAAAAAAAPP 447

Query: 271 PPPPNAQ 277
            P    Q
Sbjct: 448 APAAAPQ 454

Length = 598

>gnl|CDD|237864 PRK14950, PRK14950, DNA polymerase III subunits gamma and tau; Provisional

 Score = 39.0 bits (91), Expect = 0.002
 Identities = 20/93 (21%), Positives = 25/93 (26%), Gaps = 7/93 (7%)

Query: 171 PPVIRPPGQMPPPVYPGQGPPMARGPPPQGPPQGFGVRPPQQFPMPPQQFGQRPMVPPPP 230
           P   +P    P PV P   P                 + P +    P     RP+ PP P
Sbjct: 366 PQPAKPTAAAPSPVRPTPAPSTRPKAAAAANIPP---KEPVRETATPPPVPPRPVAPPVP 422

Query: 231 GPMMRGPPSGPPRPGMPNAPPPRPGMPPPPGAP 263
                 P S P           +P   PP    
Sbjct: 423 HT----PESAPKLTRAAIPVDEKPKYTPPAPPK 451

Length = 585

>gnl|CDD|217392 pfam03153, TFIIA, Transcription factor IIA, alpha/beta subunit

 Score = 39.0 bits (91), Expect = 0.002
 Identities = 30/168 (17%), Positives = 37/168 (22%), Gaps = 6/168 (3%)

Query: 119 PAAPLVQAQPGLAGPVRGVGGPAPGMMQPQISRPPIPQLSAPPMTYPATSGGPPVIRPPG 178
           P A L Q  P           PA    Q                  PA   GP +   PG
Sbjct: 58  PVAQLPQPLPQPPPTQALQALPAGDQQQHNTPTGSPAANPPATFALPAGPAGPTIQTEPG 117

Query: 179 QMPPPVYPGQGPPMARGPPPQGPPQGFGVRPPQQFPMPPQQFGQRPMVPPPPGPMMRGPP 238
           Q+ P   P          P   P Q    R  QQ     Q++G       P         
Sbjct: 118 QLYPVQVPVMVTQNPANSPLDQPAQQ---RALQQL---QQRYGAPASGQLPSQQQSAQKN 171

Query: 239 SGPPRPGMPNAPPPRPGMPPPPGAPVFRPGMPPPPPNAQQQQQNQQQQ 286
                   PN   P                         +Q+    + 
Sbjct: 172 DESQLQQQPNGETPPQQTDGAGDDESEALVRLREADGTLEQRIKGAEG 219

Transcription initiation factor IIA (TFIIA) is a heterotrimer, the three subunits being known as alpha, beta, and gamma, in order of molecular weight. The N and C-terminal domains of the gamma subunit are represented in pfam02268 and pfam02751, respectively. This family represents the precursor that yields both the alpha and beta subunits. The TFIIA heterotrimer is an essential general transcription initiation factor for the expression of genes transcribed by RNA polymerase II. Together with TFIID, TFIIA binds to the promoter region; this is the first step in the formation of a pre-initiation complex (PIC). Binding of the rest of the transcription machinery follows this step. After initiation, the PIC does not completely dissociate from the promoter. Some components, including TFIIA, remain attached and re-initiate a subsequent round of transcription. Length = 332

>gnl|CDD|223065 PHA03378, PHA03378, EBNA-3B; Provisional

 Score = 39.3 bits (91), Expect = 0.002
 Identities = 34/134 (25%), Positives = 40/134 (29%)

Query: 148 QISRPPIPQLSAPPMTYPATSGGPPVIRPPGQMPPPVYPGQGPPMARGPPPQGPPQGFGV 207
           QI   P         T       P  ++PP + P P+ P   PP     P     +    
Sbjct: 668 QIGHIPYQPSPTGANTMLPIQWAPGTMQPPPRAPTPMRPPAAPPGRAQRPAAATGRARPP 727

Query: 208 RPPQQFPMPPQQFGQRPMVPPPPGPMMRGPPSGPPRPGMPNAPPPRPGMPPPPGAPVFRP 267
                   PP     R   P       R P + P R   P A P  P   PPP AP    
Sbjct: 728 AAAPGRARPPAAAPGRARPPAAAPGRARPPAAAPGRARPPAAAPGAPTPQPPPQAPPAPQ 787

Query: 268 GMPPPPPNAQQQQQ 281
             P   P  Q   Q
Sbjct: 788 QRPRGAPTPQPPPQ 801

Length = 991

>gnl|CDD|237057 PRK12323, PRK12323, DNA polymerase III subunits gamma and tau; Provisional

 Score = 38.7 bits (90), Expect = 0.003
 Identities = 32/171 (18%), Positives = 39/171 (22%), Gaps = 5/171 (2%)

Query: 89  PPPPEESRAKAVSASAVAGPGIGRAAGRGVPAAPLVQAQPGLAGPVRGVGGPAPGMMQPQ 148
                 + A+   A          +A     A     A    A P       A G     
Sbjct: 416 ARAVAAAPARRSPAPEALAAARQASARGPGGAPAPAPAPA--AAPAAAARPAAAGPRPVA 473

Query: 149 ISRPPIPQLSAPPMT-YPATSGGPPVIRPPGQMPPPVYPGQGPPMARGPPPQGPPQGFGV 207
            +    P  +AP     PA    PP    P +   P  P Q      G   +  P     
Sbjct: 474 AAAAAAPARAAPAAAPAPADDDPPPWEELPPEFASPA-PAQPDAAPAGWVAESIPDPATA 532

Query: 208 RPPQQFPMPPQQFGQRPMVPPPPGPMMRGPPSGPPRPGMPNAPPPRPGMPP 258
            P   F          P  P             PPR      P    G  P
Sbjct: 533 DPDDAFETLAPAPAAAP-APRAAAATEPVVAPRPPRASASGLPDMFDGDWP 582

Length = 700

>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional

 Score = 38.4 bits (89), Expect = 0.004
 Identities = 49/184 (26%), Positives = 53/184 (28%), Gaps = 23/184 (12%)

Query: 108  PGIGRAAGRGVPAAPLVQAQPGLAGPVRGVGGPAPGMMQPQISRPPIPQLSAPPMTY--- 164
            P   R A    P A      PG  GP      PAP  + P I           P      
Sbjct: 2478 PVYRRPAEARFPFAAGAAPDPGGGGPPDPDAPPAPSRLAPAILPDEPVGEPVHPRMLTWI 2537

Query: 165  -------PATSGGPPVIRPPGQMP-------PPVYPGQGPP----MARGPPPQGPPQGFG 206
                      +G PP   PP   P       PP  P   P      +R   P  PPQ   
Sbjct: 2538 RGLEELASDDAGDPPPPLPPAAPPAAPDRSVPPPRPAPRPSEPAVTSRARRPDAPPQSAR 2597

Query: 207  VRPPQQFPMPPQQFGQRPMVPPPPGPMMRGPPSGPPRPGMPNAPPPRPGMPPPPGAPVFR 266
             R P      P+  G  P  P PP      PP   P P      P  P   PPP  P   
Sbjct: 2598 PRAPVDDRGDPR--GPAPPSPLPPDTHAPDPPPPSPSPAANEPDPHPPPTVPPPERPRDD 2655

Query: 267  PGMP 270
            P   
Sbjct: 2656 PAPG 2659

Length = 3151

>gnl|CDD|236669 PRK10263, PRK10263, DNA translocase FtsK; Provisional

 Score = 38.1 bits (88), Expect = 0.004
 Identities = 26/89 (29%), Positives = 31/89 (34%), Gaps = 1/89 (1%)

Query: 198 PQGPPQGFGVRPPQQFPMPPQQFGQRPMVPPPPGPMMRGPPSGPPRPGMPNAPPPRPGMP 257
           PQ P          Q P+ PQ   Q+P  P  P P  +  P  P  P      P +P  P
Sbjct: 755 PQQPVAPQQQYQQPQQPVAPQPQYQQPQQPVAPQPQYQ-QPQQPVAPQPQYQQPQQPVAP 813

Query: 258 PPPGAPVFRPGMPPPPPNAQQQQQNQQQQ 286
            P      +P  P P     QQ    Q Q
Sbjct: 814 QPQYQQPQQPVAPQPQYQQPQQPVAPQPQ 842

Length = 1355

>gnl|CDD|236138 PRK07994, PRK07994, DNA polymerase III subunits gamma and tau; Validated

 Score = 38.3 bits (90), Expect = 0.004
 Identities = 22/128 (17%), Positives = 29/128 (22%), Gaps = 3/128 (2%)

Query: 151 RP--PIPQLSAPPMTYPATSGGPPVIRPPGQMPPPVYPGQGPPMARGPPPQGPPQGFGVR 208
            P  P+P+   PP +    +       P   + PP  P   PP A  P            
Sbjct: 360 HPAAPLPEPEVPPQSAAPAASAQATAAPTAAVAPPQAPAVPPPPASAPQQAPAVPLPETT 419

Query: 209 PPQQFPMPPQQFGQRPMVPPPPGPMMRGPPSGPPRPGMPNAPPPRPGMPPPPGAPVFRPG 268
                     Q  Q         P        P    +      RP       AP  +  
Sbjct: 420 SQLLAARQQLQRAQGATKAKKSEPAAASRAR-PVNSALERLASVRPAPSALEKAPAKKEA 478

Query: 269 MPPPPPNA 276
                 N 
Sbjct: 479 YRWKATNP 486

Length = 647

>gnl|CDD|235906 PRK07003, PRK07003, DNA polymerase III subunits gamma and tau; Validated

 Score = 38.3 bits (89), Expect = 0.004
 Identities = 26/175 (14%), Positives = 31/175 (17%), Gaps = 6/175 (3%)

Query: 88  GPPPPEESRAKAVSASAVAGPGIGRAAGRGVPAAPLVQAQPGLAGPVRGVGGPAPGMMQP 147
            P     +     + +A A       A   V  A      P  A         AP     
Sbjct: 372 VPARVAGAVPAPGARAAAAVGASAVPAVTAVTGAAGAALAPKAAAAAAATRAEAPPAAPA 431

Query: 148 QISRPPIPQLSAPPMTYPATSGGPPVIRPPGQMPPPVYPGQGPPMARGPPPQGPPQGFGV 207
             +       +A                          P      A  P    PP     
Sbjct: 432 PPATADRGDDAADGDAPVPAKANARASADSRCDERDAQPPADSGSASAPASDAPP----- 486

Query: 208 RPPQQFPMPPQQFGQRPMVPPPPGPMMRGPPSGPPRPGMPNAPPPRPGMPPPPGA 262
                 P P             P        S    P     P P    P P  A
Sbjct: 487 -DAAFEPAPRAAAPSAATPAAVPDARAPAAASREDAPAAAAPPAPEARPPTPAAA 540

Length = 830

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	286
KOG3168	177	consensus U1 snRNP component [Transcription]	100.0
cd01717	79	Sm_B The eukaryotic Sm and Sm-like (LSm) proteins	99.92
cd06168	75	LSm9 The eukaryotic Sm and Sm-like (LSm) proteins	99.9
cd01729	81	LSm7 The eukaryotic Sm and Sm-like (LSm) proteins	99.87
cd01730	82	LSm3 The eukaryotic Sm and Sm-like (LSm) proteins	99.86
cd01727	74	LSm8 The eukaryotic Sm and Sm-like (LSm) proteins	99.86
cd01728	74	LSm1 The eukaryotic Sm and Sm-like (LSm) proteins	99.85
cd01719	72	Sm_G The eukaryotic Sm and Sm-like (LSm) proteins	99.84
cd01720	87	Sm_D2 The eukaryotic Sm and Sm-like (LSm) proteins	99.84
PRK00737	72	small nuclear ribonucleoprotein; Provisional	99.83
cd01731	68	archaeal_Sm1 The archaeal sm1 proteins: The Sm pro	99.83
cd01732	76	LSm5 The eukaryotic Sm and Sm-like (LSm) proteins	99.83
PF01423	67	LSM: LSM domain ; InterPro: IPR001163 This family	99.81
smart00651	67	Sm snRNP Sm proteins. small nuclear ribonucleoprot	99.8
cd01726	67	LSm6 The eukaryotic Sm and Sm-like (LSm) proteins	99.8
cd01722	68	Sm_F The eukaryotic Sm and Sm-like (LSm) proteins	99.79
cd00600	63	Sm_like The eukaryotic Sm and Sm-like (LSm) protei	99.78
cd01718	79	Sm_E The eukaryotic Sm and Sm-like (LSm) proteins	99.77
COG1958	79	LSM1 Small nuclear ribonucleoprotein (snRNP) homol	99.76
PTZ00138	89	small nuclear ribonucleoprotein; Provisional	99.7
cd01721	70	Sm_D3 The eukaryotic Sm and Sm-like (LSm) proteins	99.67
KOG1781	108	consensus Small Nuclear ribonucleoprotein splicing	99.66
cd01723	76	LSm4 The eukaryotic Sm and Sm-like (LSm) proteins	99.66
KOG1780	77	consensus Small Nuclear ribonucleoprotein G [RNA p	99.64
cd01724	90	Sm_D1 The eukaryotic Sm and Sm-like (LSm) proteins	99.62
cd01733	78	LSm10 The eukaryotic Sm and Sm-like (LSm) proteins	99.61
cd01725	81	LSm2 The eukaryotic Sm and Sm-like (LSm) proteins	99.58
KOG3460	91	consensus Small nuclear ribonucleoprotein (snRNP)	99.58
KOG3482	79	consensus Small nuclear ribonucleoprotein (snRNP)	99.5
KOG1784	96	consensus Small Nuclear ribonucleoprotein splicing	99.43
KOG1783	77	consensus Small nuclear ribonucleoprotein F [RNA p	99.39
KOG1782	129	consensus Small Nuclear ribonucleoprotein splicing	99.35
KOG1775	84	consensus U6 snRNA-associated Sm-like protein [RNA	99.19
KOG1774	88	consensus Small nuclear ribonucleoprotein E [RNA p	99.18
KOG3459	114	consensus Small nuclear ribonucleoprotein (snRNP)	98.88
KOG3172	119	consensus Small nuclear ribonucleoprotein Sm D3 [R	98.81
KOG3293	134	consensus Small nuclear ribonucleoprotein (snRNP)	98.8
KOG3448	96	consensus Predicted snRNP core protein [RNA proces	98.8
KOG3428	109	consensus Small nuclear ribonucleoprotein SMD1 and	98.6
cd01739	66	LSm11_C The eukaryotic Sm and Sm-like (LSm) protei	98.5
PF14438	77	SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.	97.65
PF12701	96	LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC	97.57
KOG1924	1102	consensus RhoA GTPase effector DIA/Diaphanous [Sig	97.53
KOG1924	1102	consensus RhoA GTPase effector DIA/Diaphanous [Sig	97.22
PF02237	48	BPL_C: Biotin protein ligase C terminal domain; In	96.58
PF11095	80	Gemin7: Gem-associated protein 7 (Gemin7); InterPr	96.46
PF06372	166	Gemin6: Gemin6 protein; InterPro: IPR009422 This f	96.41
cd01736	74	LSm14_N LSm14 (also known as RAP55) belongs to a f	96.37
KOG1073	361	consensus Uncharacterized mRNA-associated protein	95.71
KOG3168	177	consensus U1 snRNP component [Transcription]	95.15
PRK02001	152	hypothetical protein; Validated	94.4
cd01735	61	LSm12_N LSm12 belongs to a family of Sm-like prote	93.79
PRK14638	150	hypothetical protein; Provisional	93.76
PF10842	66	DUF2642: Protein of unknown function (DUF2642); In	93.41
PRK14639	140	hypothetical protein; Provisional	93.19
cd01716	61	Hfq Hfq, an abundant, ubiquitous RNA-binding prote	93.11
TIGR02383	61	Hfq RNA chaperone Hfq. This model represents the R	93.06
PF03614	165	Flag1_repress: Repressor of phase-1 flagellin; Int	92.52
PRK14644	136	hypothetical protein; Provisional	92.04
PRK14640	152	hypothetical protein; Provisional	91.44
cd01734	83	YlxS_C YxlS is a Bacillus subtilis gene of unknown	91.4
PRK14636	176	hypothetical protein; Provisional	91.01
PRK14642	197	hypothetical protein; Provisional	90.97
PRK14633	150	hypothetical protein; Provisional	90.92
PRK00395	79	hfq RNA-binding protein Hfq; Provisional	90.88
PRK14632	172	hypothetical protein; Provisional	90.46
PRK14646	155	hypothetical protein; Provisional	89.64
PF07073	80	ROF: Modulator of Rho-dependent transcription term	88.86
PRK14634	155	hypothetical protein; Provisional	88.61
PRK14643	164	hypothetical protein; Provisional	88.43
PRK14645	154	hypothetical protein; Provisional	88.24
PF02576	141	DUF150: Uncharacterised BCR, YhbC family COG0779;	88.14
COG0779	153	Uncharacterized protein conserved in bacteria [Fun	87.88
PRK14647	159	hypothetical protein; Provisional	87.09
PRK14637	151	hypothetical protein; Provisional	86.88
PRK14631	174	hypothetical protein; Provisional	85.84
PRK00092	154	ribosome maturation protein RimP; Reviewed	85.44
PRK06955	300	biotin--protein ligase; Provisional	85.29
PRK14641	173	hypothetical protein; Provisional	83.27
COG0340	238	BirA Biotin-(acetyl-CoA carboxylase) ligase [Coenz	83.22
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	81.9
PRK14091	165	RNA-binding protein Hfq; Provisional	80.78
PRK11886	319	bifunctional biotin--[acetyl-CoA-carboxylase] synt	80.16

>KOG3168 consensus U1 snRNP component [Transcription]

Probab=100.00  E-value=1.4e-45  Score=320.35  Aligned_cols=148  Identities=64%  Similarity=1.088  Sum_probs=139.4

Q ss_pred             CCchhhhHHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCce
Q 023166            1 MSMSKSSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEE   80 (286)
Q Consensus         1 m~~~k~skL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGen   80 (286)
                      |+++|++||+++|||+++|+|+|||+|+|+|++||+||||||+|||||++++.++.|    ..+.||||.||||+|||||
T Consensus         1 M~~a~sskml~~iNyr~rv~~qDgr~~ig~~~afDkhmNlvl~dceE~r~~k~k~~~----~~~~eEkr~lgLvllRgen   76 (177)
T KOG3168|consen    1 MTVAKSSKMLQHINYRMRVRLQDGRTFIGQFKAFDKHMNLVLQDCEEFRKIKPKNRK----MTDGEEKRVLGLVLLRGEN   76 (177)
T ss_pred             CCccchhHHHHhhcceEEEEeccCceeechhhhhHHHHHHHHHHHHHHhcccccccc----ccccceeeEEEEEEecCCc
Confidence            899999999999999999999999999999999999999999999999998876653    3578999999999999999


Q ss_pred             eEEeeecCCCCChhhhhhhccccCCCCCCccccCCCCCCCCCCcCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 023166           81 VISMTVEGPPPPEESRAKAVSASAVAGPGIGRAAGRGVPAAPLVQAQPGLAGPVRGVGGPAPGMMQPQISRPP  153 (286)
Q Consensus        81 IVSIsVe~PPp~d~~~~~~~~~~~~~Gpg~~r~aGRG~p~~~~~~~~~gL~gp~~gvggp~~~~m~p~~~~~~  153 (286)
                      |||++||++|+.|++.+++. +++..|+|++|.+||||+..++.+++.||+||++|||++++++|+|++++.+
T Consensus        77 Ivs~tVegppp~s~s~~~v~-ag~~~g~G~ar~~Grgip~~~~~~a~~gLtGp~rg~g~~a~~~~qp~g~g~p  148 (177)
T KOG3168|consen   77 IVSMTVEGPPPPSDSFRRVP-AGAARGPGIARVAGRGIPSGPLGQAPEGLTGPVRGVGGPAPQIMQPQGRGYP  148 (177)
T ss_pred             EEEEeccCCCCCcccccccc-ccccCCcccccccCCCccCCCcccCCCCCcCCccccCCCCccccCccccCCC
Confidence            99999999999999998887 8899999999999999998889999999999999999999999999987644

>cd01717 Sm_B The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.92  E-value=4.6e-25  Score=170.14  Aligned_cols=79  Identities=76%  Similarity=1.203  Sum_probs=68.7

Q ss_pred             hhhHHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEe
Q 023166            5 KSSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISM   84 (286)
Q Consensus         5 k~skL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSI   84 (286)
                      |++||++||+++|+|+|+|||+|+|+|+|||+||||||+||+|++....+..+    ..+.+++|.+|++||||+||++|
T Consensus         1 ~~~~l~~~l~~~V~V~l~dgR~~~G~L~~~D~~~NlVL~~~~E~~~~~~~~~~----~~~~~~~r~lG~v~iRG~~Vv~i   76 (79)
T cd01717           1 KSSKMLQLINYRLRVTLQDGRQFVGQFLAFDKHMNLVLSDCEEFRKVKKKKSK----NSEREEKRTLGLVLLRGENIVSM   76 (79)
T ss_pred             CcchhHHHcCCEEEEEECCCcEEEEEEEEEcCccCEEcCCEEEEEeccccccc----cccCcceeEeeeEEEcCCEEEEE
Confidence            56899999999999999999999999999999999999999999875432211    12356789999999999999999


Q ss_pred             eec
Q 023166           85 TVE   87 (286)
Q Consensus        85 sVe   87 (286)
                      +||
T Consensus        77 ~v~   79 (79)
T cd01717          77 TVE   79 (79)
T ss_pred             EEC
Confidence            986

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit B heterodimerizes with subunit D3 and three such heterodimers form a hexameric ring structure with alternating B and D3 subunits. The D3 - B heterodimer also assembles into a heptameric ring containing D1, D2, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.

>cd06168 LSm9 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.90  E-value=1.6e-23  Score=161.55  Aligned_cols=74  Identities=36%  Similarity=0.712  Sum_probs=66.3

Q ss_pred             hhHHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEee
Q 023166            6 SSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMT   85 (286)
Q Consensus         6 ~skL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIs   85 (286)
                      .++|.+||+++|+|+|+|||+|+|+|.|||+||||||+||+|++....+        ....+.|.||+++|||++|++|+
T Consensus         2 ~~~L~~~l~~~v~V~l~dgR~~~G~l~~~D~~~NivL~~~~E~~~~~~~--------~~~~~~r~lGlv~IrG~~Iv~i~   73 (75)
T cd06168           2 RQKLRSLLGRTMRIHMTDGRTLVGVFLCTDRDCNIILGSAQEYRPPPDS--------FSPTEPRVLGLVMIPGHHIVSIE   73 (75)
T ss_pred             HhHHHHhcCCeEEEEEcCCeEEEEEEEEEcCCCcEEecCcEEEEcccCc--------cCCccEEEeeeEEEeCCeEEEEE
Confidence            3689999999999999999999999999999999999999999975432        13467899999999999999999


Q ss_pred             ec
Q 023166           86 VE   87 (286)
Q Consensus        86 Ve   87 (286)
                      +|
T Consensus        74 v~   75 (75)
T cd06168          74 VE   75 (75)
T ss_pred             EC
Confidence            86

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm9 proteins have a single Sm-like domain structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.

>cd01729 LSm7 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.87  E-value=7.5e-22  Score=153.84  Aligned_cols=75  Identities=29%  Similarity=0.563  Sum_probs=63.6

Q ss_pred             hhHHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEee
Q 023166            6 SSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMT   85 (286)
Q Consensus         6 ~skL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIs   85 (286)
                      ..+|.+|||++|+|+|+|||+|+|+|++||+||||||+||+|++..+.+.      ....++++.||+++|||+||++|+
T Consensus         4 ~~~L~~~i~k~V~V~l~~gr~~~G~L~~~D~~mNlvL~~~~E~~~~~~~~------~~~~~~~~~lG~v~iRG~nV~~i~   77 (81)
T cd01729           4 ILDLSKYVDKKIRVKFQGGREVTGILKGYDQLLNLVLDDTVEYLRDPDDP------YKLTDKTRQLGLVVCRGTSVVLIS   77 (81)
T ss_pred             hhhHHHhcCCeEEEEECCCcEEEEEEEEEcCcccEEecCEEEEEccCCcc------cccccceeEccEEEEcCCEEEEEe
Confidence            35799999999999999999999999999999999999999998632211      112457889999999999999995


Q ss_pred             e
Q 023166           86 V   86 (286)
Q Consensus        86 V   86 (286)
                      .
T Consensus        78 ~   78 (81)
T cd01729          78 P   78 (81)
T ss_pred             c
Confidence            3

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm7 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.

>cd01730 LSm3 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.86  E-value=1.3e-21  Score=152.25  Aligned_cols=76  Identities=25%  Similarity=0.498  Sum_probs=62.2

Q ss_pred             HHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEee
Q 023166            9 MLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMT   85 (286)
Q Consensus         9 L~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIs   85 (286)
                      |.++++++|+|+|+|||+|+|+|++||+||||||+||+|++..+.++.+.. +....+.+|.+|++||||+||++|+
T Consensus         6 l~~~~~k~V~V~l~~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~-~~~~~~~~r~lg~~~iRGd~Vv~i~   81 (82)
T cd01730           6 IRLSLDERVYVKLRGDRELRGRLHAYDQHLNMILGDVEETITTVEIDEETY-EEIVKTTKRNIPMLFVRGDSVILVS   81 (82)
T ss_pred             HHHhCCCEEEEEECCCCEEEEEEEEEccceEEeccceEEEeeccccccccc-ccccceeEEEcCeEEEeCCEEEEEC
Confidence            567799999999999999999999999999999999999987543322100 1122457899999999999999986

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm3 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.

>cd01727 LSm8 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.86  E-value=2.2e-21  Score=148.13  Aligned_cols=71  Identities=30%  Similarity=0.501  Sum_probs=62.1

Q ss_pred             hHHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEeee
Q 023166            7 SKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMTV   86 (286)
Q Consensus         7 skL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIsV   86 (286)
                      ++|++|+|++|+|+|+|||+|+|+|++||+||||||+||+|+....          .+..+++.+|+++|||+||++|+.
T Consensus         2 ~~L~~~l~~~V~V~l~dgr~~~G~L~~~D~~~NlvL~~~~E~~~~~----------~~~~~~~~lG~~~iRG~~I~~i~~   71 (74)
T cd01727           2 STLEDYLNKTVSVITVDGRVIVGTLKGFDQATNLILDDSHERVYSS----------DEGVEQVVLGLYIIRGDNIAVVGE   71 (74)
T ss_pred             hhHHHhcCCEEEEEECCCcEEEEEEEEEccccCEEccceEEEEecC----------CCCceeeEeceEEECCCEEEEEEc
Confidence            6899999999999999999999999999999999999999986421          112467889999999999999974


Q ss_pred             c
Q 023166           87 E   87 (286)
Q Consensus        87 e   87 (286)
                      .
T Consensus        72 ~   72 (74)
T cd01727          72 I   72 (74)
T ss_pred             c
Confidence            3

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm8 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.

>cd01728 LSm1 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.85  E-value=6e-21  Score=146.98  Aligned_cols=70  Identities=27%  Similarity=0.496  Sum_probs=61.7

Q ss_pred             hhHHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEee
Q 023166            6 SSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMT   85 (286)
Q Consensus         6 ~skL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIs   85 (286)
                      ..+|++|||++|+|+|+|||+|+|+|++||+||||||+||+|+....           +...++.+|+++|||+||++|.
T Consensus         4 ~~~L~~~l~k~v~V~l~~gr~~~G~L~~fD~~~NlvL~d~~E~~~~~-----------~~~~~~~lG~~viRG~~V~~ig   72 (74)
T cd01728           4 TASLVDDLDKKVVVLLRDGRKLIGILRSFDQFANLVLQDTVERIYVG-----------DKYGDIPRGIFIIRGENVVLLG   72 (74)
T ss_pred             hHHHHHhcCCEEEEEEcCCeEEEEEEEEECCcccEEecceEEEEecC-----------CccceeEeeEEEEECCEEEEEE
Confidence            46799999999999999999999999999999999999999987632           1234688999999999999986


Q ss_pred             e
Q 023166           86 V   86 (286)
Q Consensus        86 V   86 (286)
                      .
T Consensus        73 ~   73 (74)
T cd01728          73 E   73 (74)
T ss_pred             c
Confidence            3

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm1 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.

>cd01719 Sm_G The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.84  E-value=6.5e-21  Score=145.61  Aligned_cols=69  Identities=22%  Similarity=0.552  Sum_probs=62.1

Q ss_pred             hhHHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEee
Q 023166            6 SSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMT   85 (286)
Q Consensus         6 ~skL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIs   85 (286)
                      ..+|++||||+|+|+|+|||+|+|+|++||+||||||+||+|+..              .++++.+|+++|||+||++|+
T Consensus         2 ~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~E~~~--------------~~~~~~lg~v~IRG~~I~~i~   67 (72)
T cd01719           2 PPELKKYMDKKLSLKLNGNRKVSGILRGFDPFMNLVLDDAVEVNS--------------GGEKNNIGMVVIRGNSIVMLE   67 (72)
T ss_pred             chhhHHhCCCeEEEEECCCeEEEEEEEEEcccccEEeccEEEEcc--------------CCceeEeceEEECCCEEEEEE
Confidence            468999999999999999999999999999999999999999862              134789999999999999998


Q ss_pred             ecC
Q 023166           86 VEG   88 (286)
Q Consensus        86 Ve~   88 (286)
                      ..+
T Consensus        68 ~~~   70 (72)
T cd01719          68 ALE   70 (72)
T ss_pred             ccc
Confidence            654

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit G binds subunits E and F to form a trimer which then assembles onto snRNA along with the D1/D2 and D3/B heterodimers forming a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.

>cd01720 Sm_D2 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.84  E-value=6.8e-21  Score=150.96  Aligned_cols=79  Identities=28%  Similarity=0.491  Sum_probs=63.1

Q ss_pred             HHHHhc--CCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEee
Q 023166            8 KMLQFI--NYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMT   85 (286)
Q Consensus         8 kL~qlI--gkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIs   85 (286)
                      -|.+.+  +++|+|+|+|||+|+|+|+|||+||||||+||+|++..+.+++... .....+++|++|+||||||||++|+
T Consensus         6 ~L~~~~~~~~~V~V~lr~~r~~~G~L~~fD~hmNlvL~d~~E~~~~~~k~~~~~-~~~~~~~~r~lg~v~iRGd~Vv~Is   84 (87)
T cd01720           6 LLTQAVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKTGKGK-KAKPVNKDRFISKMFLRGDSVILVL   84 (87)
T ss_pred             HHHHHHcCCCEEEEEEcCCCEEEEEEEEecCccEEEEcceEEEeeccccccccc-cccceeeeeEcccEEEeCCEEEEEe
Confidence            345665  8999999999999999999999999999999999997654332110 0123457889999999999999997


Q ss_pred             ec
Q 023166           86 VE   87 (286)
Q Consensus        86 Ve   87 (286)
                      -.
T Consensus        85 ~~   86 (87)
T cd01720          85 RN   86 (87)
T ss_pred             cC
Confidence            54

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D2 heterodimerizes with subunit D1 and three such heterodimers form a hexameric ring structure with alternating D1 and D2 subunits. The D1 - D2 heterodimer also assembles into a heptameric ring containing D2, D3, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.

>PRK00737 small nuclear ribonucleoprotein; Provisional

Probab=99.83  E-value=1.8e-20  Score=142.63  Aligned_cols=71  Identities=32%  Similarity=0.560  Sum_probs=61.2

Q ss_pred             CCchhhhHHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCce
Q 023166            1 MSMSKSSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEE   80 (286)
Q Consensus         1 m~~~k~skL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGen   80 (286)
                      |+..-...|.++++++|+|+|+|||+|+|+|++||+||||||+||+|++.              .+.++.+|+++|||+|
T Consensus         1 ~~~~P~~~L~~~~~k~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~--------------~~~~~~lg~v~iRG~~   66 (72)
T PRK00737          1 MAQRPLDVLNNALNSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEIQD--------------GEVVRKLGKVVIRGDN   66 (72)
T ss_pred             CCcchHHHHHHhCCCEEEEEECCCCEEEEEEEEEcccceeEEeeEEEEcC--------------CCeEeEcCcEEEeCCE
Confidence            44333456789999999999999999999999999999999999999742              1356889999999999


Q ss_pred             eEEee
Q 023166           81 VISMT   85 (286)
Q Consensus        81 IVSIs   85 (286)
                      |++|+
T Consensus        67 V~~i~   71 (72)
T PRK00737         67 VVYVS   71 (72)
T ss_pred             EEEEc
Confidence            99985

>cd01731 archaeal_Sm1 The archaeal sm1 proteins: The Sm proteins are conserved in all three domains of life and are always associated with U-rich RNA sequences

Probab=99.83  E-value=1.8e-20  Score=140.62  Aligned_cols=65  Identities=32%  Similarity=0.595  Sum_probs=58.9

Q ss_pred             hHHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEee
Q 023166            7 SKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMT   85 (286)
Q Consensus         7 skL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIs   85 (286)
                      +.|.+|++++|+|+|+|||+|+|+|++||+||||+|+||+|++..              .+++.+|+++|||+||++|+
T Consensus         3 ~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~--------------~~~~~lg~~~iRG~~I~~i~   67 (68)
T cd01731           3 DVLKDSLNKPVLVKLKGGKEVRGRLKSYDQHMNLVLEDAEEIDDG--------------EPVRKYGRVVIRGDNVLFIS   67 (68)
T ss_pred             HHHHHhcCCEEEEEECCCCEEEEEEEEECCcceEEEeeEEEEecC--------------CeEeEcCcEEEeCCEEEEEc
Confidence            468899999999999999999999999999999999999998641              25688999999999999985

They function to mediate RNA-RNA interactions and RNA biogenesis. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. Eukaryotic Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6). Since archaebacteria do not have any splicing apparatus, Sm proteins of archaebacteria may play a more general role. Archaeal Lsm proteins are likely to represent the ancestral Sm domain.

>cd01732 LSm5 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.83  E-value=2.2e-20  Score=144.39  Aligned_cols=69  Identities=25%  Similarity=0.492  Sum_probs=60.0

Q ss_pred             hHHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEeee
Q 023166            7 SKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMTV   86 (286)
Q Consensus         7 skL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIsV   86 (286)
                      ..|.++++++|+|+|+|||+|+|+|++||+||||||+||+|++..+           +.++++.+|+++|||+||++|+-
T Consensus         6 ~~L~~~~~~~V~V~l~~gr~~~G~L~g~D~~mNlvL~da~E~~~~~-----------~~~~~~~lg~v~iRG~nV~~i~p   74 (76)
T cd01732           6 ELIDKCIGSRIWIVMKSDKEFVGTLLGFDDYVNMVLEDVTEYEITP-----------EGRKITKLDQILLNGNNICMLVP   74 (76)
T ss_pred             HHHHHhCCCEEEEEECCCeEEEEEEEEeccceEEEEccEEEEEEcC-----------CCceeeEcCeEEEeCCeEEEEEC
Confidence            3467899999999999999999999999999999999999997411           12357889999999999999973

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm4 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.

>PF01423 LSM: LSM domain ; InterPro: IPR001163 This family is found in Lsm (like-Sm) proteins and in bacterial Lsm-related Hfq proteins

Probab=99.81  E-value=1.1e-19  Score=134.11  Aligned_cols=67  Identities=36%  Similarity=0.661  Sum_probs=61.0

Q ss_pred             hHHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEeee
Q 023166            7 SKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMTV   86 (286)
Q Consensus         7 skL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIsV   86 (286)
                      .+|+++++++|+|+|+||++|+|+|.+||+||||+|+||.|++..             ..+++.++++||||++|++|++
T Consensus         1 ~~L~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Nl~L~~~~~~~~~-------------~~~~~~~~~~~irG~~I~~I~~   67 (67)
T PF01423_consen    1 NFLQKLIGKRVRVELKNGRTYRGTLVSFDQFMNLVLSDVTETIKN-------------GPEKRSLGLVFIRGSNIRYISL   67 (67)
T ss_dssp             HHHHHTTTSEEEEEETTSEEEEEEEEEEETTEEEEEEEEEEEETT-------------ESEEEEEEEEEEEGGGEEEEEE
T ss_pred             ChhHHhCCcEEEEEEeCCEEEEEEEEEeechheEEeeeEEEEECC-------------CCcEeECcEEEEECCEEEEEEC
Confidence            368999999999999999999999999999999999999999752             1278899999999999999974

In each case, the domain adopts a core structure consisting of an open beta-barrel with an SH3-like topology. Lsm (like-Sm) proteins have diverse functions, and are thought to be important modulators of RNA biogenesis and function [, ]. The Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6) []. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker []. In other snRNPs, certain Sm proteins are replaced with different Lsm proteins, such as with U7 snRNPs, in which the D1 and D2 Sm proteins are replaced with U7-specific Lsm10 and Lsm11 proteins, where Lsm11 plays a role in histone U7-specific RNA processing []. Lsm proteins are also found in archaebacteria, which do not have any splicing apparatus suggesting a more general role for Lsm proteins. The pleiotropic translational regulator Hfq (host factor Q) is a bacterial Lsm-like protein, which modulates the structure of numerous RNA molecules by binding preferentially to A/U-rich sequences in RNA []. Hfq forms an Lsm-like fold, however, unlike the heptameric Sm proteins, Hfq forms a homo-hexameric ring.; PDB: 1D3B_K 2Y9D_D 2Y9A_D 2Y9C_R 3VRI_C 2Y9B_K 3QUI_D 3M4G_H 3INZ_E 1U1S_C ....

>smart00651 Sm snRNP Sm proteins

Probab=99.80  E-value=1.6e-19  Score=133.00  Aligned_cols=66  Identities=38%  Similarity=0.652  Sum_probs=60.1

Q ss_pred             HHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEeee
Q 023166            8 KMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMTV   86 (286)
Q Consensus         8 kL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIsV   86 (286)
                      .|++|++++|+|+|+|||+|+|+|.+||+||||+|+||+|++..             ..+.+.+++++|||++|++|+.
T Consensus         2 ~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~-------------~~~~~~~~~~~IrG~~I~~i~~   67 (67)
T smart00651        2 FLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKD-------------GEKKRKLGLVFIRGNNIVYIIL   67 (67)
T ss_pred             hhHHhCCcEEEEEECCCcEEEEEEEEECccccEEEccEEEEecC-------------CcEEeEeCCEEEcCCEEEEEeC
Confidence            68999999999999999999999999999999999999998751             1467899999999999999863

small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing

>cd01726 LSm6 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.80  E-value=2e-19  Score=134.92  Aligned_cols=64  Identities=22%  Similarity=0.390  Sum_probs=57.9

Q ss_pred             HHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEee
Q 023166            8 KMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMT   85 (286)
Q Consensus         8 kL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIs   85 (286)
                      .|.++++++|+|+|+||++|+|+|.+||.||||+|+||+|+..              ..+++.+++++|||++|++|+
T Consensus         4 ~L~~~~~~~V~V~Lk~g~~~~G~L~~~D~~mNlvL~~~~~~~~--------------~~~~~~~~~v~IRG~~I~~I~   67 (67)
T cd01726           4 FLKAIIGRPVVVKLNSGVDYRGILACLDGYMNIALEQTEEYVN--------------GQLKNKYGDAFIRGNNVLYIS   67 (67)
T ss_pred             HHHhhCCCeEEEEECCCCEEEEEEEEEccceeeEEeeEEEEeC--------------CceeeEeCCEEEECCEEEEEC
Confidence            5789999999999999999999999999999999999998752              235778999999999999985

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm6 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.

>cd01722 Sm_F The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.79  E-value=3e-19  Score=134.42  Aligned_cols=65  Identities=25%  Similarity=0.378  Sum_probs=57.9

Q ss_pred             hHHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEee
Q 023166            7 SKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMT   85 (286)
Q Consensus         7 skL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIs   85 (286)
                      ..|.++++++|+|+|+|||+|+|+|.+||+||||+|+||+|+..              ..+++.+|+++|||+||++|+
T Consensus         4 ~~L~~~~g~~V~V~Lk~g~~~~G~L~~~D~~mNi~L~~~~e~~~--------------~~~~~~lg~~~IRG~~I~~i~   68 (68)
T cd01722           4 PFLNDLTGKPVIVKLKWGMEYKGTLVSVDSYMNLQLANTEEYID--------------GKSTGNLGEVLIRCNNVLYIR   68 (68)
T ss_pred             HHHHHcCCCEEEEEECCCcEEEEEEEEECCCEEEEEeeEEEEeC--------------CccccCcCcEEEECCEEEEEC
Confidence            46789999999999999999999999999999999999998742              124678999999999999984

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit F is capable of forming both homo- and hetero-heptamer ring structures. To form the hetero-heptamer, Sm subunit F initially binds subunits E and G to form a trimer which then assembles onto snRNA along with the D3/B and D1/D2 heterodimers.

>cd00600 Sm_like The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.78  E-value=1e-18  Score=126.91  Aligned_cols=63  Identities=46%  Similarity=0.717  Sum_probs=58.0

Q ss_pred             HHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEee
Q 023166            9 MLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMT   85 (286)
Q Consensus         9 L~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIs   85 (286)
                      |.+|++++|+|+|+||++|+|+|.+||+||||+|+||+|+++.              .+.+.+++++|||++|++|+
T Consensus         1 l~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Ni~L~~~~~~~~~--------------~~~~~~~~~~irG~~I~~I~   63 (63)
T cd00600           1 LKDLVGKTVRVELKDGRVLEGVLVAFDKYMNLVLDDVEETIKE--------------GKKRVLGLVLIRGDNVRLVT   63 (63)
T ss_pred             ChHHCCCEEEEEECCCcEEEEEEEEECCCCCEEECCEEEEecC--------------CcEEECCeEEEECCEEEEEC
Confidence            5789999999999999999999999999999999999998752              46789999999999999984

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.

>cd01718 Sm_E The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.77  E-value=1.8e-18  Score=135.16  Aligned_cols=67  Identities=30%  Similarity=0.550  Sum_probs=56.7

Q ss_pred             hhHHHHhcCCEEEE--EEe--CCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCcee
Q 023166            6 SSKMLQFINYRMRV--TIQ--DGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEV   81 (286)
Q Consensus         6 ~skL~qlIgkRVRV--tLq--DGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenI   81 (286)
                      ...|.+|++++++|  .|+  +||+|+|+|++||+||||||+||+|+...             .++++.+|++||||+||
T Consensus         8 ~~~l~~~l~~~~~V~V~l~~~~g~~~~G~L~gfD~~mNlvL~d~~E~~~~-------------~~~~~~lG~iliRGnnV   74 (79)
T cd01718           8 INLIFRFLQSKQRVQIWLYEQTDLRIEGVIIGFDEYMNLVLDDAEEVHLK-------------TKTRKPLGRILLKGDNI   74 (79)
T ss_pred             HHHHHHHHccCcEEEEEEEeCCCcEEEEEEEEEccceeEEEcCEEEEecC-------------CceEeEcCcEEEeCCEE
Confidence            45788999995555  444  99999999999999999999999998741             24678899999999999


Q ss_pred             EEee
Q 023166           82 ISMT   85 (286)
Q Consensus        82 VSIs   85 (286)
                      ++|+
T Consensus        75 ~~I~   78 (79)
T cd01718          75 TLIQ   78 (79)
T ss_pred             EEEc
Confidence            9986

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit E binds subunits F and G to form a trimer which then assembles onto snRNA along with the D1/D2 and D3/B heterodimers forming a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.

>COG1958 LSM1 Small nuclear ribonucleoprotein (snRNP) homolog [Transcription]

Probab=99.76  E-value=2.9e-18  Score=131.95  Aligned_cols=71  Identities=35%  Similarity=0.575  Sum_probs=59.2

Q ss_pred             hhHHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEee
Q 023166            6 SSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMT   85 (286)
Q Consensus         6 ~skL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIs   85 (286)
                      .+.|.+++|++|.|+|+|||+|+|+|++||.||||+|+||+|++..+          .+....+..+.++|||+||++|.
T Consensus         9 ~~~l~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~----------~~~~~~~~~~~~~IRG~~I~~I~   78 (79)
T COG1958           9 LSFLKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEIISHD----------GEKNVRRLGGEVLIRGDNIVLIS   78 (79)
T ss_pred             HHHHHHhhCCEEEEEECCCCEEEEEEEEEccceeEEEeceEEEeccC----------CccccceeccEEEEECCcEEEEe
Confidence            56788999999999999999999999999999999999999987510          01113455559999999999986


Q ss_pred             e
Q 023166           86 V   86 (286)
Q Consensus        86 V   86 (286)
                      .
T Consensus        79 ~   79 (79)
T COG1958          79 P   79 (79)
T ss_pred             C
Confidence            3

>PTZ00138 small nuclear ribonucleoprotein; Provisional

Probab=99.70  E-value=7.9e-17  Score=128.58  Aligned_cols=67  Identities=30%  Similarity=0.622  Sum_probs=54.7

Q ss_pred             hHHHHhcCC--EEEEEEeC--CcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeE
Q 023166            7 SKMLQFINY--RMRVTIQD--GRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVI   82 (286)
Q Consensus         7 skL~qlIgk--RVRVtLqD--GR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIV   82 (286)
                      .++.+|+..  +|+|.|.|  +|+|+|+|++||+||||||+||+|++..             .++++.||++||||+||+
T Consensus        17 ~~~~~~~~~~~~V~i~l~~~~~r~~~G~L~gfD~~mNlVL~d~~E~~~~-------------~~~~~~lG~ilIRGnnV~   83 (89)
T PTZ00138         17 NQIFRFFTEKTRVQIWLYDHPNLRIEGKILGFDEYMNMVLDDAEEVYTK-------------KNTRKDLGRILLKGDNIT   83 (89)
T ss_pred             HHHHHHhcCCcEEEEEEEeCCCcEEEEEEEEEcccceEEEccEEEEecC-------------CceeeEcCeEEEcCCEEE
Confidence            456778876  45555656  5999999999999999999999998641             235789999999999999


Q ss_pred             Eeee
Q 023166           83 SMTV   86 (286)
Q Consensus        83 SIsV   86 (286)
                      +|+.
T Consensus        84 ~I~~   87 (89)
T PTZ00138         84 LIMA   87 (89)
T ss_pred             EEEc
Confidence            9964

>cd01721 Sm_D3 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.67  E-value=3.2e-16  Score=118.84  Aligned_cols=67  Identities=18%  Similarity=0.218  Sum_probs=57.9

Q ss_pred             hHHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEeee
Q 023166            7 SKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMTV   86 (286)
Q Consensus         7 skL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIsV   86 (286)
                      ..|.++++++|.|+|+||++|+|+|.+||.||||+|+||+|....              .+...++.++|||+||++|.+
T Consensus         3 ~~L~~~~g~~V~VeLk~g~~~~G~L~~~D~~MNl~L~~~~~~~~~--------------g~~~~~~~v~IRG~nI~~v~l   68 (70)
T cd01721           3 KLLHEAEGHIVTVELKTGEVYRGKLIEAEDNMNCQLKDVTVTARD--------------GRVSQLEQVYIRGSKIRFFIL   68 (70)
T ss_pred             HHHhhCCCCEEEEEECCCcEEEEEEEEEcCCceeEEEEEEEECCC--------------CcEeEcCcEEEeCCEEEEEEe
Confidence            346789999999999999999999999999999999999875421              123567999999999999987


Q ss_pred             c
Q 023166           87 E   87 (286)
Q Consensus        87 e   87 (286)
                      .
T Consensus        69 P   69 (70)
T cd01721          69 P   69 (70)
T ss_pred             C
Confidence            5

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D3 heterodimerizes with subunit B and three such heterodimers form a hexameric ring structure with alternating B and D3 subunits. The D3 - B heterodimer also assembles into a heptameric ring containing D1, D2, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.

>KOG1781 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]

Probab=99.66  E-value=1.4e-17  Score=135.03  Aligned_cols=75  Identities=27%  Similarity=0.531  Sum_probs=65.0

Q ss_pred             hHHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEeee
Q 023166            7 SKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMTV   86 (286)
Q Consensus         7 skL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIsV   86 (286)
                      -+|.+|+|++|||++..||+++|+|++||+.|||||+||+||.+..++..      ...++.|.||+|+|||..||+|+-
T Consensus        20 lDLsky~Dk~Irvkf~GGr~~sGiLkGyDqLlNlVLDd~vEylrdpdd~~------~~~~~tR~LGLvV~RGTalvlisp   93 (108)
T KOG1781|consen   20 LDLSKYLDKKIRVKFTGGREASGILKGYDQLLNLVLDDTVEYLRDPDDPY------KLTDETRKLGLVVCRGTALVLISP   93 (108)
T ss_pred             hhHHHhhccceEEEeecCceeeeehhhHHHHHHHHHHHHHHHhcCCCCcc------chhhhhheeeeEEEcccEEEEEcC
Confidence            46889999999999999999999999999999999999999987544322      234566999999999999999964


Q ss_pred             c
Q 023166           87 E   87 (286)
Q Consensus        87 e   87 (286)
                      .
T Consensus        94 ~   94 (108)
T KOG1781|consen   94 A   94 (108)
T ss_pred             C
Confidence            4

>cd01723 LSm4 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.66  E-value=3.7e-16  Score=120.11  Aligned_cols=68  Identities=19%  Similarity=0.264  Sum_probs=58.3

Q ss_pred             HHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEeeec
Q 023166            8 KMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMTVE   87 (286)
Q Consensus         8 kL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIsVe   87 (286)
                      -|.++++++|.|+|+||++|+|+|.+||.||||+|+||+|...             +.+....++.++|||++|++|++.
T Consensus         5 ~L~~~~g~~V~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~~-------------~g~~~~~~~~v~IRG~~I~~i~~p   71 (76)
T cd01723           5 LLKTAQNHPMLVELKNGETYNGHLVNCDNWMNIHLREVICTSK-------------DGDKFWKMPECYIRGNTIKYLRVP   71 (76)
T ss_pred             HHHhcCCCEEEEEECCCCEEEEEEEEEcCCCceEEEeEEEECC-------------CCcEeeeCCcEEEeCCEEEEEEcC
Confidence            4678999999999999999999999999999999999998632             122345679999999999999876


Q ss_pred             C
Q 023166           88 G   88 (286)
Q Consensus        88 ~   88 (286)
                      +
T Consensus        72 ~   72 (76)
T cd01723          72 D   72 (76)
T ss_pred             H
Confidence            4

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm4 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.

>KOG1780 consensus Small Nuclear ribonucleoprotein G [RNA processing and modification]

Probab=99.64  E-value=3.1e-16  Score=121.40  Aligned_cols=74  Identities=23%  Similarity=0.519  Sum_probs=63.4

Q ss_pred             CCchhhhHHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCce
Q 023166            1 MSMSKSSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEE   80 (286)
Q Consensus         1 m~~~k~skL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGen   80 (286)
                      |+.+--.+|++|+||+|.|+|+.||.+.|+|++||.||||||+||.|...              .+.+..+|.++|||++
T Consensus         1 Msksg~PeLkkymdKki~lklnG~r~v~GiLrGyD~FmNiVlde~vE~~~--------------~~~~~~ig~~vIrgns   66 (77)
T KOG1780|consen    1 MSKSGHPELKKYMDKKIVLKLNGGRKVTGILRGYDPFMNIVLDETVEPNG--------------DGDKNNIGMVVIRGNS   66 (77)
T ss_pred             CCcccCchHHHhhhheEEEEeCCCcEEEEEEeccchHHhhhhhhceeecC--------------cCCcceeeeEEEeccE
Confidence            44442259999999999999999999999999999999999999999753              2456789999999999


Q ss_pred             eEEeeecC
Q 023166           81 VISMTVEG   88 (286)
Q Consensus        81 IVSIsVe~   88 (286)
                      |+.++..+
T Consensus        67 iv~~eaL~   74 (77)
T KOG1780|consen   67 IVMVEALE   74 (77)
T ss_pred             EEEEeecc
Confidence            99986543

>cd01724 Sm_D1 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.62  E-value=1.9e-15  Score=120.34  Aligned_cols=73  Identities=15%  Similarity=0.256  Sum_probs=62.6

Q ss_pred             HHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEeeec
Q 023166            8 KMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMTVE   87 (286)
Q Consensus         8 kL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIsVe   87 (286)
                      .|.++++++|+|+|+||++|+|+|.++|.||||+|+||+|+..              ......++.++|||+||++|++.
T Consensus         5 fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~a~~~~~--------------~~~~~~~~~v~IRG~nI~yi~lP   70 (90)
T cd01724           5 FLMKLTNETVTIELKNGTIVHGTITGVDPSMNTHLKNVKLTLK--------------GRNPVPLDTLSIRGNNIRYFILP   70 (90)
T ss_pred             HHHhCCCCEEEEEECCCCEEEEEEEEEcCceeEEEEEEEEEcC--------------CCceeEcceEEEeCCEEEEEEcC
Confidence            4678999999999999999999999999999999999998753              12456799999999999999998


Q ss_pred             CCCCChh
Q 023166           88 GPPPPEE   94 (286)
Q Consensus        88 ~PPp~d~   94 (286)
                      +---.|.
T Consensus        71 d~l~~~~   77 (90)
T cd01724          71 DSLNLDT   77 (90)
T ss_pred             CcCCcch
Confidence            7543333

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D1 heterodimerizes with subunit D2 and three such heterodimers form a hexameric ring structure with alternating D1 and D2 subunits. The D1 - D2 heterodimer also assembles into a heptameric ring containing DB, D3, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.

>cd01733 LSm10 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.61  E-value=2.2e-15  Score=117.04  Aligned_cols=64  Identities=11%  Similarity=0.284  Sum_probs=56.3

Q ss_pred             HHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEeee
Q 023166            9 MLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMTV   86 (286)
Q Consensus         9 L~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIsV   86 (286)
                      |.+++|++|.|+|+||.+|+|+|.++|.||||+|+||+|...              ...+..++.++|||+||++|++
T Consensus        14 L~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~~~~~~~--------------~~~~~~~~~v~IRG~nI~yI~l   77 (78)
T cd01733          14 LQGLQGKVVTVELRNETTVTGRIASVDAFMNIRLAKVTIIDR--------------NGKQVQVEEIMVTGRNIRYVHI   77 (78)
T ss_pred             HHHCCCCEEEEEECCCCEEEEEEEEEcCCceeEEEEEEEEcC--------------CCceeECCcEEEECCEEEEEEc
Confidence            567899999999999999999999999999999999987642              1234478999999999999986

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm10 is an SmD1-like protein which is thought to bind U7 snRNA along with LSm11 and five other Sm subunits to form a 7-member ring structure. LSm10 and the U7 snRNP of which it is a part are thought to play an important role in histone mRNA 3' processing.

>cd01725 LSm2 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.58  E-value=6.4e-15  Score=114.84  Aligned_cols=70  Identities=13%  Similarity=0.186  Sum_probs=58.9

Q ss_pred             hHHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEeee
Q 023166            7 SKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMTV   86 (286)
Q Consensus         7 skL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIsV   86 (286)
                      +.|.++++++|.|+|+||++|+|+|.++|.||||+|+||+++....            ......++.++|||++|++|++
T Consensus         4 ~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNi~L~n~~~~~~~~------------~~~~~~~~~v~IRG~~I~~I~l   71 (81)
T cd01725           4 SFFKTLVGKEVTVELKNDLSIRGTLHSVDQYLNIKLTNISVTDPEK------------YPHMLSVKNCFIRGSVVRYVQL   71 (81)
T ss_pred             HHHHhCCCCEEEEEECCCcEEEEEEEEECCCcccEEEEEEEEcCCC------------cccccccCeEEEECCEEEEEEe
Confidence            3578899999999999999999999999999999999998764210            1124456999999999999987


Q ss_pred             cC
Q 023166           87 EG   88 (286)
Q Consensus        87 e~   88 (286)
                      .+
T Consensus        72 p~   73 (81)
T cd01725          72 PA   73 (81)
T ss_pred             Ch
Confidence            65

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm2 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.

>KOG3460 consensus Small nuclear ribonucleoprotein (snRNP) LSM3 [RNA processing and modification]

Probab=99.58  E-value=3.4e-16  Score=123.76  Aligned_cols=82  Identities=28%  Similarity=0.492  Sum_probs=64.7

Q ss_pred             chhhhHHH-HhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCcee
Q 023166            3 MSKSSKML-QFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEV   81 (286)
Q Consensus         3 ~~k~skL~-qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenI   81 (286)
                      |...-+|+ -+++.||.|+|+++|+++|+|.|||+|+|+||+|++|.....+.+..+ .+...++.+|.+-.+||||++|
T Consensus         3 v~ePldllrlsLdErVyVKlr~drel~G~L~afD~HlNmvL~d~eetit~~e~~E~~-~e~~~k~~~r~~emlFvRGd~V   81 (91)
T KOG3460|consen    3 VEEPLDLLRLSLDERVYVKLRSDRELRGTLHAFDEHLNMVLGDVEETITTVEIDEDT-YEEIVKTTKRTVEMLFVRGDGV   81 (91)
T ss_pred             ccccHHHHhhcccceEEEEecCChhhhcchhhhHHhhhhhhhhhhheEEEeeccchh-HHHHHhhhhcceeEEEEeCCeE
Confidence            33444555 479999999999999999999999999999999999998764322110 1122457789999999999999


Q ss_pred             EEee
Q 023166           82 ISMT   85 (286)
Q Consensus        82 VSIs   85 (286)
                      +.|+
T Consensus        82 ilvs   85 (91)
T KOG3460|consen   82 ILVS   85 (91)
T ss_pred             EEEc
Confidence            9983

>KOG3482 consensus Small nuclear ribonucleoprotein (snRNP) SMF [RNA processing and modification]

Probab=99.50  E-value=3e-14  Score=110.28  Aligned_cols=69  Identities=22%  Similarity=0.364  Sum_probs=61.7

Q ss_pred             chhhhHHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeE
Q 023166            3 MSKSSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVI   82 (286)
Q Consensus         3 ~~k~skL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIV   82 (286)
                      ++-+..|+.+++|+|+|+|+.|.+|+|+|.+.|.||||.|.+||||+.              .+..-.||.|+||++||.
T Consensus         7 vNPKpFL~~l~gk~V~vkLKwg~eYkG~LvsvD~YmNlqL~~~eE~id--------------G~~~g~lGEilIRCNNvl   72 (79)
T KOG3482|consen    7 VNPKPFLNGLTGKPVLVKLKWGQEYKGTLVSVDNYMNLQLANAEEYID--------------GVSTGNLGEILIRCNNVL   72 (79)
T ss_pred             CCchHHHhhccCCeEEEEEecCcEEEEEEEEecchhheehhhhhhhhc--------------ccccccceeEEEEeccEE
Confidence            455678999999999999999999999999999999999999999974              234567999999999999


Q ss_pred             Eee
Q 023166           83 SMT   85 (286)
Q Consensus        83 SIs   85 (286)
                      +|.
T Consensus        73 yi~   75 (79)
T KOG3482|consen   73 YIR   75 (79)
T ss_pred             EEe
Confidence            984

>KOG1784 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]

Probab=99.43  E-value=8.7e-14  Score=111.61  Aligned_cols=71  Identities=31%  Similarity=0.512  Sum_probs=62.4

Q ss_pred             hHHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEeee
Q 023166            7 SKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMTV   86 (286)
Q Consensus         7 skL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIsV   86 (286)
                      +.|..|+|+||.|...|||.|+|+|++||+..||+|+||.|....          ..+..+...||+-+||||||.+|-.
T Consensus         3 s~L~~y~n~~V~vIt~DGr~ivgsLkGFDq~tNlii~~~heRi~s----------~~~gv~q~~lGlyiirgeNva~ig~   72 (96)
T KOG1784|consen    3 STLEDYMNQRVSVITNDGRVIVGSLKGFDQTTNLIIDESHERIFS----------ETEGVEQIVLGLYIIRGENVAVIGE   72 (96)
T ss_pred             hhHHHHhhceEEEEecCCeEEEEEeccccccceeeehhhHhhhhh----------hhcchhheeeEEEEEecCccceeee
Confidence            579999999999999999999999999999999999999997651          1245677899999999999999854


Q ss_pred             c
Q 023166           87 E   87 (286)
Q Consensus        87 e   87 (286)
                      -
T Consensus        73 i   73 (96)
T KOG1784|consen   73 I   73 (96)
T ss_pred             c
Confidence            3

>KOG1783 consensus Small nuclear ribonucleoprotein F [RNA processing and modification]

Probab=99.39  E-value=8.1e-14  Score=107.83  Aligned_cols=69  Identities=20%  Similarity=0.391  Sum_probs=62.5

Q ss_pred             hhHHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEee
Q 023166            6 SSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMT   85 (286)
Q Consensus         6 ~skL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIs   85 (286)
                      ...|.++|++.|.|+|.||-.|+|+|.|+|-||||.|+.++|+..              ..++++.|.+||||+||.+|+
T Consensus         8 ~~fl~~iiGr~V~VKl~sgvdyrG~l~~lDgymNiaLe~tee~~n--------------gql~n~ygdaFirGnnVlyIs   73 (77)
T KOG1783|consen    8 GEFLKAIIGRTVVVKLNSGVDYRGTLVCLDGYMNIALESTEEYVN--------------GQLKNKYGDAFIRGNNVLYIS   73 (77)
T ss_pred             HHHHHHHhCCeEEEEecCCccccceehhhhhHHHHHHHHHHHHhc--------------CcccccccceeeccccEEEEE
Confidence            567889999999999999999999999999999999999999863              246788999999999999998


Q ss_pred             ecC
Q 023166           86 VEG   88 (286)
Q Consensus        86 Ve~   88 (286)
                      .+.
T Consensus        74 ~~~   76 (77)
T KOG1783|consen   74 TQK   76 (77)
T ss_pred             ecc
Confidence            763

>KOG1782 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]

Probab=99.35  E-value=1.1e-13  Score=116.19  Aligned_cols=70  Identities=27%  Similarity=0.478  Sum_probs=60.4

Q ss_pred             hHHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEeee
Q 023166            7 SKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMTV   86 (286)
Q Consensus         7 skL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIsV   86 (286)
                      ..|.+|+++++.|.|+|||.+.|.|++||+|.||||.+|.|.+....           .--.+-.|+.+|||||||.|-.
T Consensus        12 ~sl~~~~dkKllVlLRDGR~L~G~LRSfDQFaNlvL~~~iERi~v~~-----------~Y~di~~glfiIRGENVvllGe   80 (129)
T KOG1782|consen   12 TSLVEYLDKKLLVLLRDGRKLIGVLRSFDQFANLVLQGVIERIFVGN-----------KYCDIPRGLFIIRGENVVLLGE   80 (129)
T ss_pred             hHHHHHhcceEEEEEecCcchhhhhhhHHHHHHHHHHhhhhheeecc-----------eecccCceEEEEecCcEEEEec
Confidence            45899999999999999999999999999999999999999887532           2234567999999999999864


Q ss_pred             c
Q 023166           87 E   87 (286)
Q Consensus        87 e   87 (286)
                      .
T Consensus        81 i   81 (129)
T KOG1782|consen   81 I   81 (129)
T ss_pred             C
Confidence            3

>KOG1775 consensus U6 snRNA-associated Sm-like protein [RNA processing and modification]

Probab=99.19  E-value=1.1e-11  Score=96.88  Aligned_cols=68  Identities=25%  Similarity=0.518  Sum_probs=57.5

Q ss_pred             HHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEeeecC
Q 023166           10 LQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMTVEG   88 (286)
Q Consensus        10 ~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIsVe~   88 (286)
                      -+.|+.+|.|.+++.|+|+|||++||.|.|+||+|+.||....           +......+++++|.|+||..+.--+
T Consensus        13 DkcIgski~iimksdkE~~GtL~GFDd~VNmvLeDvtEye~~~-----------egr~~tk~~~iLLnGNni~mLvPGG   80 (84)
T KOG1775|consen   13 DKCIGSKIWIIMKSDKEFVGTLVGFDDFVNMVLEDVTEYEITP-----------EGRRMTKLDQILLNGNNITMLVPGG   80 (84)
T ss_pred             HHhcCceEEEEEccCceeeeEEechHHHHHHHHHhhhheeeCC-----------CcceeeeeeeeeecCCcEEEEecCC
Confidence            4788999999999999999999999999999999999997632           2234567899999999998775433

>KOG1774 consensus Small nuclear ribonucleoprotein E [RNA processing and modification]

Probab=99.18  E-value=1.5e-11  Score=97.20  Aligned_cols=68  Identities=35%  Similarity=0.659  Sum_probs=53.9

Q ss_pred             hHHHHhcCCEEEEEE----eCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeE
Q 023166            7 SKMLQFINYRMRVTI----QDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVI   82 (286)
Q Consensus         7 skL~qlIgkRVRVtL----qDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIV   82 (286)
                      ..+.+||..+.+|++    +-+-.+.|++.+||+||||||+|++|... +            +...+.||.++|+||||.
T Consensus        15 n~Ifr~Lq~~t~VqIWl~eq~~~rieG~IvGFDEyMNvVlD~aeev~~-k------------~~~rk~lGRilLKGDnIt   81 (88)
T KOG1774|consen   15 NLIFRFLQNRTRVQIWLFEQVGLRIEGRIVGFDEYMNLVLDDAEEVHS-K------------TKSRKELGRILLKGDNIT   81 (88)
T ss_pred             HHHHHHHhcCCceEEEEEeccCcEEeEEEechHHhhhhhhcchhhccc-c------------ccCCCccccEEEcCCcEE
Confidence            456688887666654    45888999999999999999999999764 1            122348999999999999


Q ss_pred             Eeeec
Q 023166           83 SMTVE   87 (286)
Q Consensus        83 SIsVe   87 (286)
                      .|.-.
T Consensus        82 li~~~   86 (88)
T KOG1774|consen   82 LIQSA   86 (88)
T ss_pred             EEeec
Confidence            98643

>KOG3459 consensus Small nuclear ribonucleoprotein (snRNP) Sm core protein [RNA processing and modification]

Probab=98.88  E-value=3.8e-10  Score=93.37  Aligned_cols=70  Identities=29%  Similarity=0.510  Sum_probs=57.6

Q ss_pred             CEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEee
Q 023166           15 YRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMT   85 (286)
Q Consensus        15 kRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIs   85 (286)
                      ..|.|.++|++.+.|.+.|||.|+|++|+|+.|.+....++++... ....+..|++|.+|||||+|+.+.
T Consensus        37 ~~vLi~cRnn~k~l~Rv~afdrhcnmvlenvkelwte~~ks~kgkk-~~~~~~~r~isK~flRGdsvI~v~  106 (114)
T KOG3459|consen   37 TQVLINCRNNVKLLGRVKAFDRHCNMVLENVKELWTEVPKSGKGKK-AKPVNKDRFISKMFLRGDSVILVL  106 (114)
T ss_pred             ceeEEEecccHHHHhhhhhhhccccchhhcHHHHCCccccCCCccc-CCccchhhhhheeeecCCeEEEEE
Confidence            4677888999999999999999999999999999988766544211 122455899999999999998875

>KOG3172 consensus Small nuclear ribonucleoprotein Sm D3 [RNA processing and modification]

Probab=98.81  E-value=1.7e-08  Score=83.68  Aligned_cols=74  Identities=22%  Similarity=0.293  Sum_probs=60.7

Q ss_pred             CCchhhhHHH-HhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCc
Q 023166            1 MSMSKSSKML-QFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGE   79 (286)
Q Consensus         1 m~~~k~skL~-qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGe   79 (286)
                      |+++-.-||+ +.-++.|.|++..|..|.|.|.-.|++||+.|+|..-...    +          .....|..|||||+
T Consensus         1 ~s~gvpiKlLhEaqGhIVt~Et~tGe~YRGkliEaeDnmNcql~di~vT~~----d----------g~vs~le~V~IRGS   66 (119)
T KOG3172|consen    1 MSVGVPIKLLHEAQGHIVTVETKTGEVYRGKLIEAEDNMNCQLRDITVTAR----D----------GRVSQLEQVFIRGS   66 (119)
T ss_pred             CccccceeeeecccCcEEEEEecCCceeeeeeEEeccccccEEEEEEEEcc----C----------CcceeeeeEEEecC
Confidence            4566566655 6778899999999999999999999999999999987653    1          23446789999999


Q ss_pred             eeEEeeecC
Q 023166           80 EVISMTVEG   88 (286)
Q Consensus        80 nIVSIsVe~   88 (286)
                      .|.++.+.+
T Consensus        67 ~IRFlvlPd   75 (119)
T KOG3172|consen   67 KIRFLVLPD   75 (119)
T ss_pred             eEEEEECch
Confidence            999998765

>KOG3293 consensus Small nuclear ribonucleoprotein (snRNP) [RNA processing and modification]

Probab=98.80  E-value=8.8e-09  Score=86.99  Aligned_cols=69  Identities=17%  Similarity=0.239  Sum_probs=59.0

Q ss_pred             HHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEeeec
Q 023166            8 KMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMTVE   87 (286)
Q Consensus         8 kL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIsVe   87 (286)
                      -|...-+..|.|+|++|.+|.|.|+..|.+|||.|.|++++..             +......+..+.|||++|.+|.++
T Consensus         6 LL~~aq~~pmlvELKNget~nGhL~~cD~wMNl~L~~Vi~ts~-------------Dgdkf~r~pEcYirGttIkylri~   72 (134)
T KOG3293|consen    6 LLKTAQNHPMLVELKNGETYNGHLVNCDNWMNLHLREVICTSE-------------DGDKFFRMPECYIRGTTIKYLRIP   72 (134)
T ss_pred             HHHhcCCCeEEEEecCCCEecceeecchhhhhcchheeEEecc-------------CCCceeecceeEEecceeEEEecc
Confidence            3455678999999999999999999999999999999998753             223456778999999999999988


Q ss_pred             CC
Q 023166           88 GP   89 (286)
Q Consensus        88 ~P   89 (286)
                      +.
T Consensus        73 d~   74 (134)
T KOG3293|consen   73 DE   74 (134)
T ss_pred             HH
Confidence            64

>KOG3448 consensus Predicted snRNP core protein [RNA processing and modification]

Probab=98.80  E-value=2.1e-08  Score=80.59  Aligned_cols=70  Identities=16%  Similarity=0.201  Sum_probs=58.8

Q ss_pred             hHHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEeee
Q 023166            7 SKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMTV   86 (286)
Q Consensus         7 skL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIsV   86 (286)
                      +....+|+++|.|+|+++-.|.|||.++|+|+||.|.|.......            ..-.--.+-.+||||+.|.+|.+
T Consensus         5 sfFkslvg~~V~VeLKnd~~i~GtL~svDqyLNlkL~di~v~d~~------------kyPhm~Sv~ncfIRGSvvrYv~l   72 (96)
T KOG3448|consen    5 SFFKSLVGKEVVVELKNDLSICGTLHSVDQYLNLKLTDISVTDPD------------KYPHMLSVKNCFIRGSVVRYVQL   72 (96)
T ss_pred             HHHHHhcCCeEEEEEcCCcEEEEEecccchhheeEEeeeEeeCcc------------cCCCeeeeeeEEEeccEEEEEEe
Confidence            456789999999999999999999999999999999998765321            12345567789999999999988


Q ss_pred             cC
Q 023166           87 EG   88 (286)
Q Consensus        87 e~   88 (286)
                      ..
T Consensus        73 ~k   74 (96)
T KOG3448|consen   73 PK   74 (96)
T ss_pred             Ch
Confidence            75

>KOG3428 consensus Small nuclear ribonucleoprotein SMD1 and related snRNPs [RNA processing and modification]

Probab=98.60  E-value=3e-07  Score=76.18  Aligned_cols=73  Identities=16%  Similarity=0.251  Sum_probs=61.0

Q ss_pred             hHHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEeee
Q 023166            7 SKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMTV   86 (286)
Q Consensus         7 skL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIsV   86 (286)
                      ..|.++.+.++.|+|+|++++.|++.++|.+||..|.++.-..+               .+-..+-.+.|||+||.++.+
T Consensus         5 r~L~kl~~e~vtIeLkngt~v~G~I~~Vd~~Mn~~l~~v~~t~~---------------~~pv~l~~lsirgnniRy~~l   69 (109)
T KOG3428|consen    5 RFLKKLLNERVTIELKNGTIVHGTIDSVDVQMNTHLKHVKMTVK---------------GEPVRLDTLSIRGNNIRYYIL   69 (109)
T ss_pred             HHHHHhhCCeEEEEecCCcEEeeeEEEEEhhheeEEEEEEEecC---------------CCceeEEEEEeecceEEEEEc
Confidence            35778899999999999999999999999999999999976532               123567789999999999998


Q ss_pred             cCCCCChh
Q 023166           87 EGPPPPEE   94 (286)
Q Consensus        87 e~PPp~d~   94 (286)
                      .+.-.-|.
T Consensus        70 pD~l~ld~   77 (109)
T KOG3428|consen   70 PDSLNLDT   77 (109)
T ss_pred             cCCcCcce
Confidence            88665554

>cd01739 LSm11_C The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=98.50  E-value=4.8e-08  Score=74.52  Aligned_cols=41  Identities=29%  Similarity=0.414  Sum_probs=32.4

Q ss_pred             HhcC--CEEEEEEeCC----cEEEEEEEEeccccceEeCceEEeecC
Q 023166           11 QFIN--YRMRVTIQDG----RQLVGKFMAFDRHMNLVLGDCEEFRKL   51 (286)
Q Consensus        11 qlIg--kRVRVtLqDG----R~fvGtLlAFDKhMNLVLsD~eE~r~i   51 (286)
                      +++.  .||+|.++.-    -.++|.|+|||||+||+|.|++|.++.
T Consensus         3 ~~~~er~RVrV~iR~~~gvrG~~~G~lvAFDK~wNm~L~DV~E~y~~   49 (66)
T cd01739           3 RCVQERIRVRVHIRTFKGLRGVCSGFLVAFDKFWNMALVDVDETYRK   49 (66)
T ss_pred             hhhhCCcEEEEEEecccCcccEEEEEEEeeeeehhheehhhhhhhcc
Confidence            4445  5777777532    267899999999999999999999874

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm11 is an SmD2 - like subunit which binds U7 snRNA along with LSm10 and five other Sm subunits to form a 7-member ring structure. LSm11 and the U7 snRNP of which it is a part are thought to play an important role in histone mRNA 3' processing.

>PF14438 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1

Probab=97.65  E-value=7.7e-05  Score=56.94  Aligned_cols=67  Identities=15%  Similarity=0.302  Sum_probs=39.5

Q ss_pred             HHHhcCCEEEEEEeCCcEEEEEEEEecc---ccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeE
Q 023166            9 MLQFINYRMRVTIQDGRQLVGKFMAFDR---HMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVI   82 (286)
Q Consensus         9 L~qlIgkRVRVtLqDGR~fvGtLlAFDK---hMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIV   82 (286)
                      +..+|+++|.|+++||.+|+|.|.+++.   .+.++|+.+.+......+       +...........++|+++.|+
T Consensus         7 ~~~lvG~~V~V~~~~G~~yeGif~s~s~~~~~~~vvLk~a~~~~~~~~~-------~~~~~~~~~~~tlii~~~dvv   76 (77)
T PF14438_consen    7 LTNLVGQTVEVTTKNGSVYEGIFHSASPESNEFDVVLKMARKVPKSDQS-------NSDPLSSEIVETLIIPAKDVV   76 (77)
T ss_dssp             HHTTTTSEEEEEETTS-EEEEEEEEE-T---T--EEEEEEEETTS-------------EEEEEEE-GGGEEE-----
T ss_pred             HHhCcCCEEEEEECCCCEEEEEEEeCCCcccceeEEEEeeeeccccccc-------cCCccCCCCCceEEEeccccC
Confidence            5679999999999999999999999998   889999888765431110       011223334456677777665

>PF12701 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC8_A 2VXF_A 2VXE_A

Probab=97.57  E-value=0.00019  Score=58.42  Aligned_cols=79  Identities=16%  Similarity=0.370  Sum_probs=59.8

Q ss_pred             HHHhcCCEEEEEEeCCcEEEEEEEEecc-ccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEeeec
Q 023166            9 MLQFINYRMRVTIQDGRQLVGKFMAFDR-HMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMTVE   87 (286)
Q Consensus         9 L~qlIgkRVRVtLqDGR~fvGtLlAFDK-hMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIsVe   87 (286)
                      ..+||+++|.++.+++-.|+|+|..+|. .-+|.|.|+.-|-...++...     ..--.+..+..|++||+.|..|.|.
T Consensus         3 ~~~~IGs~ISlisk~~iRYeG~L~~Id~~~sTItL~nVr~~GtE~R~~~~-----~ipp~~~v~~~I~Fr~sDIkdL~v~   77 (96)
T PF12701_consen    3 ADPYIGSKISLISKSDIRYEGILYSIDTEDSTITLKNVRSFGTEGRPTDR-----EIPPSDEVYDYIVFRGSDIKDLKVI   77 (96)
T ss_dssp             CCCCTTCEEEEEETTTEEEEEEEEEEETTTTEEEEEEEEETTETTSS-SS--------C-CSSSSEEEEETTTEEEEEEC
T ss_pred             cccccCCEEEEEECCCcEEEEEEEEEcCCCCEEEeeeeeecCcCCCCcCc-----ccCCCCceeeEEEEEccccceEEEE
Confidence            4589999999999999999999999996 689999999888764322111     1122345677999999999999999


Q ss_pred             CCCCC
Q 023166           88 GPPPP   92 (286)
Q Consensus        88 ~PPp~   92 (286)
                      +.+..
T Consensus        78 e~~~~   82 (96)
T PF12701_consen   78 EPPPP   82 (96)
T ss_dssp             E-S-S
T ss_pred             cCCCC
Confidence            87664

>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]

Probab=97.53  E-value=0.00053  Score=72.81  Aligned_cols=20  Identities=45%  Similarity=0.984  Sum_probs=9.3

Q ss_pred             CCCCCCCCCCCCCCCCCCCC
Q 023166          232 PMMRGPPSGPPRPGMPNAPP  251 (286)
Q Consensus       232 ~~~~~~p~~p~~~~~~~~~~  251 (286)
                      +++.||||||+++|+.||||
T Consensus       565 g~aG~PPpPppppg~~gppP  584 (1102)
T KOG1924|consen  565 GIAGGPPPPPPPPGGGGPPP  584 (1102)
T ss_pred             cccCCCCccCCCCCCCCCCC
Confidence            34444444444455554333

>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]

Probab=97.22  E-value=0.003  Score=67.33  Aligned_cols=25  Identities=52%  Similarity=1.060  Sum_probs=11.0

Q ss_pred             CCCCCCCCCCCCCCC--CCCCCCCCCC
Q 023166          234 MRGPPSGPPRPGMPN--APPPRPGMPP  258 (286)
Q Consensus       234 ~~~~p~~p~~~~~~~--~~~~~~~~~~  258 (286)
                      ..||||||+..|-.|  ||||.++|.+
T Consensus       579 ~~gppPPPpp~g~~Gg~ppPP~~gm~p  605 (1102)
T KOG1924|consen  579 GGGPPPPPPPGGFLGGPPPPPPPGMFP  605 (1102)
T ss_pred             CCCCCCcCCCCCCCCCCCCCCCCCccc
Confidence            334443333344444  4444555555

>PF02237 BPL_C: Biotin protein ligase C terminal domain; InterPro: IPR003142 This C-terminal domain has an SH3-like barrel fold, the function of which is unknown

Probab=96.58  E-value=0.0061  Score=43.05  Aligned_cols=35  Identities=14%  Similarity=0.180  Sum_probs=30.7

Q ss_pred             hcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEE
Q 023166           12 FINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEE   47 (286)
Q Consensus        12 lIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE   47 (286)
                      +||++|+|++ ++..++|+++++|.+-+|+|.+...
T Consensus         1 ~lG~~V~v~~-~~~~~~G~~~gId~~G~L~v~~~~g   35 (48)
T PF02237_consen    1 TLGQEVRVET-GDGEIEGIAEGIDDDGALLVRTEDG   35 (48)
T ss_dssp             STTSEEEEEE-TSCEEEEEEEEEETTSEEEEEETTE
T ss_pred             CCCCEEEEEE-CCeEEEEEEEEECCCCEEEEEECCC
Confidence            5899999999 6777899999999999999976554

It is found associated with prokaryotic bifunctional transcriptional repressors [] and eukaryotic enzymes involved in biotin utilization [, ]. In Escherichia coli the biotin operon repressor (BirA) is a bifunctional protein. BirA acts both as the acetyl-coA carboxylase biotin holoenzyme synthetase (6.3.4.15 from EC) and as the biotin operon repressor. DNA sequence analysis of mutations indicates that the helix-turn-helix DNA binding region is located at the N terminus while mutations affecting enzyme function, although mapping over a large region, are found mainly in the central part of the protein's primary sequence [].; GO: 0006464 protein modification process; PDB: 3RUX_A 2CGH_A 3L1A_B 3L2Z_A 1HXD_A 1BIB_A 2EWN_B 1BIA_A 2EJ9_A 3FJP_A ....

>PF11095 Gemin7: Gem-associated protein 7 (Gemin7); InterPro: IPR020338 Gem-associated protein 7 (Gemin7) is a component of the survival of motor neuron complex, which functions in the assembly of spliceosomal small nuclear ribonucleoproteins

Probab=96.46  E-value=0.013  Score=46.60  Aligned_cols=62  Identities=19%  Similarity=0.325  Sum_probs=43.9

Q ss_pred             HHHHhcCCEEEEEEeCCcEEEEEEEEeccc-cceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEeee
Q 023166            8 KMLQFINYRMRVTIQDGRQLVGKFMAFDRH-MNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMTV   86 (286)
Q Consensus         8 kL~qlIgkRVRVtLqDGR~fvGtLlAFDKh-MNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIsV   86 (286)
                      .|+...++.|.++|.++.++.|+|.++|.. .|+..+|-+                   .---.....+||...|+++++
T Consensus        18 ~l~~~~gk~v~f~l~e~t~V~a~F~a~d~~~~~f~Vs~L~-------------------TPlGv~~eAlLR~~DVi~~~f   78 (80)
T PF11095_consen   18 SLLAMVGKPVEFTLHENTTVSARFGACDIDVSNFQVSNLQ-------------------TPLGVQPEALLRCSDVISISF   78 (80)
T ss_dssp             HHHHCTTSEEEEEEGGG-EEEEEEEEE-TTS-EEEEEEEE-------------------TTTTEEEEEEEEGGGEEEEEE
T ss_pred             HHHHhcCCceEEEEeCCeEEEEEEEEecCchheEEhhhcC-------------------CCcccChhheeecCCEEEEEe
Confidence            366788999999999999999999999954 455544332                   112235678999999999998


Q ss_pred             cC
Q 023166           87 EG   88 (286)
Q Consensus        87 e~   88 (286)
                      +.
T Consensus        79 ~~   80 (80)
T PF11095_consen   79 DA   80 (80)
T ss_dssp             --
T ss_pred             cC
Confidence            73

Gemin7 interacts with several Sm proteins of spliceosomal small nuclear ribonucleoproteins, especially SmE []. Gem-associated protein 7 is found in the nucleoplasm, in nuclear "gems" (Gemini of Cajal bodies), and in the cytoplasm. Three transcript variants encoding the same protein have been found for this gene [].; GO: 0032797 SMN complex; PDB: 1Y96_D.

>PF06372 Gemin6: Gemin6 protein; InterPro: IPR009422 This family consists of several mammalian Gemin6 proteins

Probab=96.41  E-value=0.0091  Score=53.05  Aligned_cols=63  Identities=21%  Similarity=0.352  Sum_probs=44.0

Q ss_pred             hhHHHHhcCCEEEEEEeCCcEEEEEEEEec-cccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEe
Q 023166            6 SSKMLQFINYRMRVTIQDGRQLVGKFMAFD-RHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISM   84 (286)
Q Consensus         6 ~skL~qlIgkRVRVtLqDGR~fvGtLlAFD-KhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSI   84 (286)
                      ...+.+|++|.|+|++.| +++.|.|..+| ---||||.+-.|-                  .++.  .-+|-|.+|.+|
T Consensus         9 p~~~~~yv~K~VkV~~~d-~~~~G~v~TiDPVS~siVL~~~~e~------------------~~~s--v~~I~ghaVk~v   67 (166)
T PF06372_consen    9 PLEWQDYVGKEVKVTLSD-KEYKGWVYTIDPVSASIVLVNFQED------------------GKRS--VKVIMGHAVKSV   67 (166)
T ss_dssp             HHHHHCTTT-EEEEEETT-EEEEEEEEEE-TTT--EEEEEE-TT------------------S-EE--EEEE-GGGEEEE
T ss_pred             HHHHHHhhCcEEEEEEec-cEEEEEEEEeCCCCCeEEEEEcccC------------------Ccee--EEEEEccceEEE
Confidence            356789999999999999 99999999999 4468998854331                  1222  467779999999


Q ss_pred             eecCC
Q 023166           85 TVEGP   89 (286)
Q Consensus        85 sVe~P   89 (286)
                      ++...
T Consensus        68 evl~~   72 (166)
T PF06372_consen   68 EVLSE   72 (166)
T ss_dssp             EEEE-
T ss_pred             EEccC
Confidence            98774

The exact function of Gemin6 is unknown but it has been found to form part of the Survival of motor neuron complex. The SMN complex plays a key role in the biogenesis of spliceosomal small nuclear ribonucleoproteins (snRNPs) and other ribonucleoprotein particles [].; GO: 0000245 spliceosome assembly, 0005634 nucleus; PDB: 1Y96_A.

>cd01736 LSm14_N LSm14 (also known as RAP55) belongs to a family of Sm-like proteins that associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=96.37  E-value=0.015  Score=45.66  Aligned_cols=71  Identities=10%  Similarity=0.249  Sum_probs=53.3

Q ss_pred             HHhcCCEEEEEEeCCcEEEEEEEEeccc-cceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEe
Q 023166           10 LQFINYRMRVTIQDGRQLVGKFMAFDRH-MNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISM   84 (286)
Q Consensus        10 ~qlIgkRVRVtLqDGR~fvGtLlAFDKh-MNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSI   84 (286)
                      .+||+++|.+..+.+-.|+|+|..+|.+ --|.|.|+..|-...++...    .+.--.......|+.||+.|..+
T Consensus         2 ~~~IG~~isLISk~~iRYeGiL~~In~~~sTi~L~nVr~fGTEgR~~~~----~~ipp~~~vyd~IvFrgsDIkDL   73 (74)
T cd01736           2 TPYIGSKISLISKSDIRYEGILYTINTEDSTIALKNVRSFGTEGRPTDG----PEIPPSDEVYDYIVFRGSDIKDL   73 (74)
T ss_pred             ccccCceEEEEecCCcEEEEEEEeeccccCEEEeeeeEeecccCCCCCC----CccCCCCcceeEEEEcCCccccc
Confidence            4799999999999999999999999966 46779999988775432211    01112345667899999998765

Members of this family share a highly conserved Sm fold, containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet, that associates with other Sm proteins to form hexameric and heptameric ring structures. In addition to the N-terminal Sm-like domain, LSm14 has an uncharacterized C-terminal domain containing a conserved DFDF box. In Xenopus laevis, LSm14 is an oocyte-specific constituent of ribonucleoprotein particles.

>KOG1073 consensus Uncharacterized mRNA-associated protein RAP55 [Intracellular trafficking, secretion, and vesicular transport]

Probab=95.71  E-value=0.027  Score=55.50  Aligned_cols=79  Identities=14%  Similarity=0.310  Sum_probs=63.0

Q ss_pred             HHHhcCCEEEEEEeCCcEEEEEEEEec-cccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEeeec
Q 023166            9 MLQFINYRMRVTIQDGRQLVGKFMAFD-RHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMTVE   87 (286)
Q Consensus         9 L~qlIgkRVRVtLqDGR~fvGtLlAFD-KhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIsVe   87 (286)
                      +..||+++|.++-+....|+|+|.-+| +..=|-|.++.-|-+..+|+.   ...+-...| +..-||.||+.|..|.|+
T Consensus         4 ~t~yIGS~ISLISk~DIRYEGILy~in~qdSTlgLqnVRsfGTEgRk~~---~pq~p~~~k-Vy~YIlFRGSDIKDL~V~   79 (361)
T KOG1073|consen    4 VTSYIGSFISLISKNDIRYEGILYTINLQDSTLGLQNVRSFGTEGRKTD---GPQVPPDDK-VYDYILFRGSDIKDLIVQ   79 (361)
T ss_pred             ccccccceeEEeecccceeeeEEEeccccccceehhheeecccccCCCC---CCcCCCCcc-ceeeEEecCcccceeeec
Confidence            468999999999999999999999999 667899999887776544321   122334455 889999999999999999


Q ss_pred             CCCC
Q 023166           88 GPPP   91 (286)
Q Consensus        88 ~PPp   91 (286)
                      +.|.
T Consensus        80 ~~p~   83 (361)
T KOG1073|consen   80 ETPA   83 (361)
T ss_pred             cCcc
Confidence            8554

>KOG3168 consensus U1 snRNP component [Transcription]

Probab=95.15  E-value=0.093  Score=47.02  Aligned_cols=73  Identities=15%  Similarity=0.078  Sum_probs=54.7

Q ss_pred             hHHHHhcCCEEEEE-EeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEe
Q 023166            7 SKMLQFINYRMRVT-IQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISM   84 (286)
Q Consensus         7 skL~qlIgkRVRVt-LqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSI   84 (286)
                      .++++|.+.+.++. +.|+++.++.++++|+-.|||+..+|++-...++..+     .-..+.+.+|+-.+.|..|++.
T Consensus        43 ~dceE~r~~k~k~~~~~~~eEkr~lgLvllRgenIvs~tVegppp~s~s~~~-----v~ag~~~g~G~ar~~Grgip~~  116 (177)
T KOG3168|consen   43 QDCEEFRKIKPKNRKMTDGEEKRVLGLVLLRGENIVSMTVEGPPPPSDSFRR-----VPAGAARGPGIARVAGRGIPSG  116 (177)
T ss_pred             HHHHHHhccccccccccccceeeEEEEEEecCCcEEEEeccCCCCCcccccc-----ccccccCCcccccccCCCccCC
Confidence            45667778777775 8999999999999999999999999998653221110     1134567788888888888874

>PRK02001 hypothetical protein; Validated

Probab=94.40  E-value=0.14  Score=44.69  Aligned_cols=39  Identities=15%  Similarity=0.352  Sum_probs=33.1

Q ss_pred             hhhhHHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeC
Q 023166            4 SKSSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLG   43 (286)
Q Consensus         4 ~k~skL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLs   43 (286)
                      .+...+.+|+++.|+|+|.|++.|+|+|.+||.. +++|.
T Consensus        80 ~~~~~f~r~~G~~v~V~l~~~~~~~G~L~~~~~~-~i~l~  118 (152)
T PRK02001         80 KVPRQYKKNIGRELEVLTKNGKKIEGELKSADEN-DITLE  118 (152)
T ss_pred             CCHHHHHHhCCCEEEEEECCCCEEEEEEEEEeCC-EEEEE
Confidence            3456788999999999999999999999999976 45553

>cd01735 LSm12_N LSm12 belongs to a family of Sm-like proteins that associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=93.79  E-value=0.11  Score=39.32  Aligned_cols=36  Identities=17%  Similarity=0.312  Sum_probs=30.6

Q ss_pred             hcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEE
Q 023166           12 FINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEE   47 (286)
Q Consensus        12 lIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE   47 (286)
                      +|+.+|+|++..|.+|+|.+.|||.-.+++.-.|.+
T Consensus         4 ~iGs~V~~kTc~g~~ieGEV~afD~~tk~lIlk~~s   39 (61)
T cd01735           4 SVGSQVSCRTCFEQRLQGEVVAFDYPSKMLILKCPS   39 (61)
T ss_pred             ccccEEEEEecCCceEEEEEEEecCCCcEEEEECcc
Confidence            578999999999999999999999887776555544

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet that associates with other Sm proteins to form hexameric and heptameric ring structures. In addition to the N-terminal Sm-like domain, LSm12 has a novel methyltransferase domain.

>PRK14638 hypothetical protein; Provisional

Probab=93.76  E-value=0.16  Score=44.10  Aligned_cols=39  Identities=13%  Similarity=0.417  Sum_probs=33.0

Q ss_pred             hhhhHHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeC
Q 023166            4 SKSSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLG   43 (286)
Q Consensus         4 ~k~skL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLs   43 (286)
                      -+..++.+|++++|+|+|.+++.|+|+|.++|.. +|+|.
T Consensus        90 ~~~~~f~r~~G~~v~V~~~~~k~~~G~L~~~~~~-~i~l~  128 (150)
T PRK14638         90 RGPKDYVRFTGKLAKIVTKDGKTFIGRIESFVDG-TITIS  128 (150)
T ss_pred             CCHHHHHHhCCCEEEEEECCCcEEEEEEEEEeCC-EEEEE
Confidence            3566788999999999999999999999999964 45553

>PF10842 DUF2642: Protein of unknown function (DUF2642); InterPro: IPR020139 This entry contains proteins with no known function

Probab=93.41  E-value=0.29  Score=37.61  Aligned_cols=51  Identities=16%  Similarity=0.275  Sum_probs=37.1

Q ss_pred             HHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEee
Q 023166            8 KMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMT   85 (286)
Q Consensus         8 kL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIs   85 (286)
                      .|+++++++|.|++..|+. .|+|++..-. .|+|+.+.                         ..++||=.+|++|.
T Consensus        15 ~lq~liG~~vvV~T~~g~v-~G~L~~V~pD-hIvl~~~~-------------------------~~~~IR~~~IV~v~   65 (66)
T PF10842_consen   15 TLQSLIGQRVVVQTTRGSV-RGILVDVKPD-HIVLEENG-------------------------TPFFIRIAQIVWVM   65 (66)
T ss_pred             HHHHhcCCEEEEEEcCCcE-EEEEEeecCC-EEEEEeCC-------------------------cEEEEEeeeEEEEc
Confidence            4789999999999977665 9999997522 23443331                         24678888888874

>PRK14639 hypothetical protein; Provisional

Probab=93.19  E-value=0.2  Score=42.99  Aligned_cols=39  Identities=23%  Similarity=0.384  Sum_probs=33.1

Q ss_pred             hhhhHHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeC
Q 023166            4 SKSSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLG   43 (286)
Q Consensus         4 ~k~skL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLs   43 (286)
                      -+..++.+|+++.|+|+|.+++.|+|+|+++|.. +++|.
T Consensus        78 ~~~~~f~r~~G~~v~v~l~~~~~~~G~L~~~~~~-~i~l~  116 (140)
T PRK14639         78 SKIEHFAKSIGELVKITTNEKEKFEGKIVSVDDE-NITLE  116 (140)
T ss_pred             CCHHHHHHhCCCEEEEEECCCcEEEEEEEEEeCC-EEEEE
Confidence            3456788999999999999999999999999985 55553

>cd01716 Hfq Hfq, an abundant, ubiquitous RNA-binding protein, functions as a pleiotrophic regulator of RNA metabolism in prokaryotes, required for transcription of some transcripts and degradation of others

Probab=93.11  E-value=0.17  Score=38.38  Aligned_cols=30  Identities=23%  Similarity=0.397  Sum_probs=24.7

Q ss_pred             CCEEEEEEeCCcEEEEEEEEeccccceEeC
Q 023166           14 NYRMRVTIQDGRQLVGKFMAFDRHMNLVLG   43 (286)
Q Consensus        14 gkRVRVtLqDGR~fvGtLlAFDKhMNLVLs   43 (286)
                      +..|.|-|.||-.++|++++||+|+=|+-+
T Consensus        11 ~~~Vtv~L~NG~~l~G~I~~fD~ftVll~~   40 (61)
T cd01716          11 KIPVTIYLVNGVQLKGQIESFDNFTVLLES   40 (61)
T ss_pred             CCcEEEEEeCCcEEEEEEEEEcceEEEEEE
Confidence            456778889999999999999999855533

Hfq binds small RNA molecules called riboregulators that modulate the stability or translation efficiency of RNA transcripts. Hfq binds preferentially to unstructured A/U-rich RNA sequences and is similar to the eukaryotic Sm proteins in both sequence and structure. Hfq forms a homo-hexameric ring similar to the heptameric ring of the Sm proteins.

>TIGR02383 Hfq RNA chaperone Hfq

Probab=93.06  E-value=0.17  Score=38.38  Aligned_cols=29  Identities=28%  Similarity=0.363  Sum_probs=24.1

Q ss_pred             CCEEEEEEeCCcEEEEEEEEeccccceEe
Q 023166           14 NYRMRVTIQDGRQLVGKFMAFDRHMNLVL   42 (286)
Q Consensus        14 gkRVRVtLqDGR~fvGtLlAFDKhMNLVL   42 (286)
                      ...|.|-|.+|-.++|++++||+|+=|+-
T Consensus        15 ~~~Vti~L~nG~~l~G~I~~fD~ftVll~   43 (61)
T TIGR02383        15 RIPVTVFLVNGVQLKGVIESFDNFTVLLE   43 (61)
T ss_pred             CCcEEEEEeCCcEEEEEEEEEeeeEEEEE
Confidence            34677778999999999999999985543

This model represents the RNA-binding pleiotropic regulator Hfq, a small, Sm-like protein of bacteria. It helps pair regulatory noncoding RNAs with complementary mRNA target regions. It enhances the elongation of poly(A) tails on mRNA. It appears also to protect RNase E recognition sites (A/U-rich sequences with adjacent stem-loop structures) from cleavage. Being pleiotropic, it differs in some of its activities in different species. Hfq binds the non-coding regulatory RNA DsrA (see Rfam RF00014) in the few species known to have it: Escherichia coli, Shigella flexneri, Salmonella spp. In Azorhizobium caulinodans, an hfq mutant is unable to express nifA, and Hfq is called NrfA, for nif regulatory factor (see PubMed:8197116). The name hfq reflects phenomenology as a host factor for phage Q-beta RNA replication.

>PF03614 Flag1_repress: Repressor of phase-1 flagellin; InterPro: IPR003223 Flagellin is the subunit which polymerises to form the filaments of bacterial flagella

Probab=92.52  E-value=0.12  Score=45.75  Aligned_cols=75  Identities=17%  Similarity=0.145  Sum_probs=48.6

Q ss_pred             hHHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCC--CCCCcccccceeEeceEEecCceeE
Q 023166            7 SKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGK--KNNTNEEREDRRTLGLVLLRGEEVI   82 (286)
Q Consensus         7 skL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~k--k~~~~~e~eekR~LGlVLIRGenIV   82 (286)
                      -+..++-+.-|||++.||.+|.|++.+||.--|.||+-.. +.+.+.-.-+  ...+-++.......|..+|+.+.+.
T Consensus        22 l~f~r~~~~pVrvv~~ng~~f~myV~gf~~~~n~iL~p~~-~~~~nRi~~plE~I~t~Ee~~~~d~~g~~ti~~d~~~   98 (165)
T PF03614_consen   22 LQFWRFNDIPVRVVSENGQVFCMYVSGFMSKENKILAPDP-FKKENRIRLPLERISTIEELIVSDFKGRLTIHPDYFN   98 (165)
T ss_pred             HHHHHhcCCceEEEecCCcEEEEEEeccCcccCEEeccCC-CCCCceEEEEhHHhhhHhhhccccccccEEechhhcc
Confidence            3445677889999999999999999999999999998765 3221110000  0001122333445677777777553

The proteins in this family are transcriptional repressors of phase-1 flagellin genes.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent

>PRK14644 hypothetical protein; Provisional

Probab=92.04  E-value=0.34  Score=41.60  Aligned_cols=36  Identities=11%  Similarity=0.272  Sum_probs=31.0

Q ss_pred             hHHHHhcCCEEEEEEeCC----cEEEEEEEEeccccceEeC
Q 023166            7 SKMLQFINYRMRVTIQDG----RQLVGKFMAFDRHMNLVLG   43 (286)
Q Consensus         7 skL~qlIgkRVRVtLqDG----R~fvGtLlAFDKhMNLVLs   43 (286)
                      .++.+|+++.|+|+|++.    ++|+|+|.++|.. +++|.
T Consensus        78 ~~f~r~~G~~v~V~l~~~~~~~~~~~G~L~~v~~~-~i~l~  117 (136)
T PRK14644         78 DELENHIGEIIDVSLNKEVNKTDFITGELLENNPE-TITLK  117 (136)
T ss_pred             HHHHHhCCCeEEEEEccCcCCeEEEEEEEEEEeCC-EEEEE
Confidence            478999999999999877    9999999999975 56554

>PRK14640 hypothetical protein; Provisional

Probab=91.44  E-value=0.55  Score=40.76  Aligned_cols=39  Identities=18%  Similarity=0.311  Sum_probs=32.0

Q ss_pred             hhhhHHHHhcCCEEEEEE----eCCcEEEEEEEEeccccceEeC
Q 023166            4 SKSSKMLQFINYRMRVTI----QDGRQLVGKFMAFDRHMNLVLG   43 (286)
Q Consensus         4 ~k~skL~qlIgkRVRVtL----qDGR~fvGtLlAFDKhMNLVLs   43 (286)
                      -+...+.+|++++|+|+|    .+.+.|+|+|.++|.. ++.|.
T Consensus        87 ~~~~~f~r~~G~~v~V~l~~~~~~~k~~~G~L~~v~~~-~v~l~  129 (152)
T PRK14640         87 FKVAQFEKYVGQEAAVTLRMATNNRRKFKGVIKAVQGD-MITLT  129 (152)
T ss_pred             CCHHHHHHhCCCeEEEEEecccCCceEEEEEEEEEeCC-EEEEE
Confidence            356678899999999999    5779999999999875 45543

>cd01734 YlxS_C YxlS is a Bacillus subtilis gene of unknown function with two domains that each have an alpha/beta fold

Probab=91.40  E-value=0.7  Score=35.90  Aligned_cols=37  Identities=19%  Similarity=0.437  Sum_probs=30.4

Q ss_pred             hhhHHHHhcCCEEEEEEe---CC-cEEEEEEEEeccccceEe
Q 023166            5 KSSKMLQFINYRMRVTIQ---DG-RQLVGKFMAFDRHMNLVL   42 (286)
Q Consensus         5 k~skL~qlIgkRVRVtLq---DG-R~fvGtLlAFDKhMNLVL   42 (286)
                      +..++.+|+++.|.|+|+   +| +.|+|+|.++|.. +++|
T Consensus        16 ~~~~~~r~~G~~v~v~~~~~~~~~~~~~G~L~~~~~~-~v~l   56 (83)
T cd01734          16 KEADFERAVGKYVHVKLYQPIDGQKEFEGTLLGVDDD-TVTL   56 (83)
T ss_pred             CHHHHHHhCCCEEEEEEEcccCCeEEEEEEEEeEeCC-EEEE
Confidence            456788999999999997   55 6899999999985 4554

The N-terminal domain is composed of two alpha-helices and a three-stranded beta-sheet, while the C-terminal domain is composed of one alpha-helix and a five-stranded beta-sheet. This CD represents the C-terminal domain which has a fold similar to the Sm fold of proteins like Sm-D3.

>PRK14636 hypothetical protein; Provisional

Probab=91.01  E-value=0.48  Score=42.30  Aligned_cols=38  Identities=16%  Similarity=0.478  Sum_probs=30.8

Q ss_pred             hhhhHHHHhcCCEEEEEEe---CC-cEEEEEEEEeccccceEe
Q 023166            4 SKSSKMLQFINYRMRVTIQ---DG-RQLVGKFMAFDRHMNLVL   42 (286)
Q Consensus         4 ~k~skL~qlIgkRVRVtLq---DG-R~fvGtLlAFDKhMNLVL   42 (286)
                      -+...+.+|+++.|+|+|+   || +.|+|+|.++|.. +++|
T Consensus        88 ~~~~df~r~~G~~V~V~l~~~~~g~k~~~G~L~~v~~~-~v~l  129 (176)
T PRK14636         88 TRPKDFADWAGHEARIALSEPLDGRKQFRGELKGIDGD-TVTI  129 (176)
T ss_pred             CCHHHHHHhCCCeEEEEEecccCCeEEEEEEEEEEeCC-EEEE
Confidence            3567789999999999997   55 6999999999874 4544

>PRK14642 hypothetical protein; Provisional

Probab=90.97  E-value=0.5  Score=43.20  Aligned_cols=38  Identities=8%  Similarity=0.238  Sum_probs=31.7

Q ss_pred             hhhhHHHHhcCCEEEEEEe-------------CCcEEEEEEEEeccccceEe
Q 023166            4 SKSSKMLQFINYRMRVTIQ-------------DGRQLVGKFMAFDRHMNLVL   42 (286)
Q Consensus         4 ~k~skL~qlIgkRVRVtLq-------------DGR~fvGtLlAFDKhMNLVL   42 (286)
                      -+..++.+|+++.|.|+|+             +.+.|+|+|.++|.. +|.|
T Consensus        90 k~~~df~rfiG~~V~V~l~~pi~~~~~~~~~~~rk~f~G~L~~~~~~-~i~l  140 (197)
T PRK14642         90 RHEQDFERFAGEVIDITLKAPIGAAAGGQVSANRKKFRGTLERAESG-GWQI  140 (197)
T ss_pred             CCHHHHHHhCCCeEEEEEeccccccccccccCCceEEEEEEEEEcCC-EEEE
Confidence            3567789999999999998             789999999999875 4444

>PRK14633 hypothetical protein; Provisional

Probab=90.92  E-value=0.47  Score=41.12  Aligned_cols=39  Identities=8%  Similarity=0.246  Sum_probs=32.0

Q ss_pred             hhhhHHHHhcCCEEEEEE----eCCcEEEEEEEEeccccceEeC
Q 023166            4 SKSSKMLQFINYRMRVTI----QDGRQLVGKFMAFDRHMNLVLG   43 (286)
Q Consensus         4 ~k~skL~qlIgkRVRVtL----qDGR~fvGtLlAFDKhMNLVLs   43 (286)
                      -+..++.+|++++|+|++    .+.+.|+|+|..+|.. +|.|.
T Consensus        84 ~~~~~f~r~~G~~v~V~~~~~~~~~~~~~G~L~~v~~~-~i~l~  126 (150)
T PRK14633         84 FNIIQAQALVGFNVKAVTLAPVGSQTKFKGVLERVEGN-NVILN  126 (150)
T ss_pred             CCHHHHHHhCCCeEEEEEecccCCcEEEEEEEEEEeCC-EEEEE
Confidence            356678899999999998    4789999999999876 45553

>PRK00395 hfq RNA-binding protein Hfq; Provisional

Probab=90.88  E-value=0.51  Score=37.57  Aligned_cols=31  Identities=19%  Similarity=0.389  Sum_probs=25.2

Q ss_pred             CCEEEEEEeCCcEEEEEEEEeccccceEeCc
Q 023166           14 NYRMRVTIQDGRQLVGKFMAFDRHMNLVLGD   44 (286)
Q Consensus        14 gkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD   44 (286)
                      ...|.|-|.+|-.+.|++++||+|+=|+-+|
T Consensus        19 ~~~VtifL~NG~~l~G~I~~fD~ftVll~~~   49 (79)
T PRK00395         19 RVPVTIYLVNGIKLQGQIESFDNFVVLLRNT   49 (79)
T ss_pred             CCCEEEEEeCCcEEEEEEEEEccEEEEEEEC
Confidence            3467778899999999999999998555444

>PRK14632 hypothetical protein; Provisional

Probab=90.46  E-value=0.56  Score=41.63  Aligned_cols=39  Identities=21%  Similarity=0.487  Sum_probs=31.8

Q ss_pred             hhhhHHHHhcCCEEEEEEeC-------CcEEEEEEEEeccccceEeC
Q 023166            4 SKSSKMLQFINYRMRVTIQD-------GRQLVGKFMAFDRHMNLVLG   43 (286)
Q Consensus         4 ~k~skL~qlIgkRVRVtLqD-------GR~fvGtLlAFDKhMNLVLs   43 (286)
                      -+...+.+|+++.|+|+|.+       .+.|+|+|+.+|.. +|+|.
T Consensus        88 ~~~~~f~r~iG~~V~V~l~~~~~~~~g~k~~~G~L~~v~~~-~i~l~  133 (172)
T PRK14632         88 FRAEQMSPYVGRQIELTLIDPTPEWPGRRKFRGELLAVEGD-TVVLR  133 (172)
T ss_pred             CCHHHHHHhCCCEEEEEEeccccccCCceEEEEEEEEEeCC-EEEEE
Confidence            35667889999999999976       68999999999864 55553

>PRK14646 hypothetical protein; Provisional

Probab=89.64  E-value=1  Score=39.32  Aligned_cols=38  Identities=13%  Similarity=0.267  Sum_probs=30.6

Q ss_pred             hhhhHHHHhcCCEEEEEEeC----CcEEEEEEEEeccccceEe
Q 023166            4 SKSSKMLQFINYRMRVTIQD----GRQLVGKFMAFDRHMNLVL   42 (286)
Q Consensus         4 ~k~skL~qlIgkRVRVtLqD----GR~fvGtLlAFDKhMNLVL   42 (286)
                      -+..++.+|++++|+|+|++    .+.|+|+|++||.. +|.|
T Consensus        90 ~~~~df~r~~G~~v~V~l~~~~~~~~~~~G~L~~~~~~-~v~l  131 (155)
T PRK14646         90 TSERDFKTFKGFPVNVELNQKNSKIKFLNGLLYEKSKD-YLAI  131 (155)
T ss_pred             CCHHHHHHhCCCEEEEEEecCcCCeEEEEEEEEEEeCC-EEEE
Confidence            35667899999999999953    37889999999986 4555

>PF07073 ROF: Modulator of Rho-dependent transcription termination (ROF); InterPro: IPR009778 This family consists of several bacterial modulator of Rho-dependent transcription termination (ROF) proteins

Probab=88.86  E-value=0.36  Score=38.18  Aligned_cols=60  Identities=28%  Similarity=0.391  Sum_probs=30.0

Q ss_pred             HHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEeeecC
Q 023166            9 MLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMTVEG   88 (286)
Q Consensus         9 L~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIsVe~   88 (286)
                      |.=.-+|+|+++|+||.++.|+  |.|-..|-   +-+|+..+.                ..-+...||=++|++|++..
T Consensus        12 iAC~~~~~v~L~l~dG~~~~g~--A~dt~~~~---~k~E~L~l~----------------~~~~~~~i~Ld~I~~~~al~   70 (80)
T PF07073_consen   12 IACMYRYPVKLTLKDGEQIEGK--ALDTRTNA---KKEECLVLE----------------QDGGEQEIRLDQIASMSALT   70 (80)
T ss_dssp             HHHTTTT-EEEE-TTT--EEES--S-EEE------SSS-EEEEE----------------ETTEEEEESTT--SEEE---
T ss_pred             HHHhcCCeEEEEEeCCCEEEEE--EEEEEEec---CceEEEEEe----------------cCCcEEEEEhhheeeeeecC
Confidence            4445689999999999999998  44432221   445554431                11245678889999998665


Q ss_pred             C
Q 023166           89 P   89 (286)
Q Consensus        89 P   89 (286)
                      +
T Consensus        71 ~   71 (80)
T PF07073_consen   71 D   71 (80)
T ss_dssp             -
T ss_pred             C
Confidence            3

ROF binds transcription termination factor Rho and inhibits Rho-dependent termination in vivo [].; PDB: 1SG5_A.

>PRK14634 hypothetical protein; Provisional

Probab=88.61  E-value=1.3  Score=38.59  Aligned_cols=38  Identities=18%  Similarity=0.379  Sum_probs=30.7

Q ss_pred             hhhhHHHHhcCCEEEEEEeC----CcEEEEEEEEeccccceEe
Q 023166            4 SKSSKMLQFINYRMRVTIQD----GRQLVGKFMAFDRHMNLVL   42 (286)
Q Consensus         4 ~k~skL~qlIgkRVRVtLqD----GR~fvGtLlAFDKhMNLVL   42 (286)
                      -+..++.+|+++.|+|+|.+    .+.|+|+|+++|.. +|.|
T Consensus        90 ~~~~~f~r~~G~~V~V~l~~~~~~~k~~~G~L~~~~~~-~v~l  131 (155)
T PRK14634         90 SSDRDFQTFRGFPVEVSHRDDDGSEQRLEGLLLERNED-HLQI  131 (155)
T ss_pred             CCHHHHHHhCCCeEEEEEecCCCCeEEEEEEEEEEeCC-EEEE
Confidence            35678899999999999863    38999999999875 4555

>PRK14643 hypothetical protein; Provisional

Probab=88.43  E-value=0.99  Score=39.87  Aligned_cols=34  Identities=9%  Similarity=0.284  Sum_probs=29.3

Q ss_pred             hhhhHHHHhcCCEEEEEEeC----CcEEEEEEEEeccc
Q 023166            4 SKSSKMLQFINYRMRVTIQD----GRQLVGKFMAFDRH   37 (286)
Q Consensus         4 ~k~skL~qlIgkRVRVtLqD----GR~fvGtLlAFDKh   37 (286)
                      -+..++.+|+++.|+|+|++    .+.|+|+|+++|..
T Consensus        94 ~~~~df~r~~G~~V~V~l~~~~~g~k~~~G~L~~~~~~  131 (164)
T PRK14643         94 RSQEELVKALNQWVYVQLNNEIKKVKEFEGYVTKYNVN  131 (164)
T ss_pred             CCHHHHHHhcCCeEEEEEecccCCceEEEEEEEEEeCC
Confidence            35677899999999999965    69999999999865

>PRK14645 hypothetical protein; Provisional

Probab=88.24  E-value=1.3  Score=38.79  Aligned_cols=38  Identities=13%  Similarity=0.300  Sum_probs=31.2

Q ss_pred             hhhhHHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeC
Q 023166            4 SKSSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLG   43 (286)
Q Consensus         4 ~k~skL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLs   43 (286)
                      -+..++.+|+++.|+|++ +++.|+|+|+++|.. +|+|.
T Consensus        92 ~~~~df~r~~G~~v~v~~-~~k~~~G~L~~~~d~-~i~l~  129 (154)
T PRK14645         92 FTARHFERFAGLKAKVRG-PGENFTGRIKAVSGD-QVTFD  129 (154)
T ss_pred             CCHHHHHHhCCCEEEEEc-CCeEEEEEEEEEeCC-EEEEE
Confidence            356678899999999986 899999999999875 45553

>PF02576 DUF150: Uncharacterised BCR, YhbC family COG0779; InterPro: IPR003728 The RimP protein facilitates maturation of the 30S ribsomal subunit, and is required for the efficient production of translationally competent ribosmomes []

Probab=88.14  E-value=0.81  Score=38.64  Aligned_cols=37  Identities=19%  Similarity=0.507  Sum_probs=27.9

Q ss_pred             hhhHHHHhcCCEEEEEE----eCCcEEEEEEEEeccccceEe
Q 023166            5 KSSKMLQFINYRMRVTI----QDGRQLVGKFMAFDRHMNLVL   42 (286)
Q Consensus         5 k~skL~qlIgkRVRVtL----qDGR~fvGtLlAFDKhMNLVL   42 (286)
                      +..++.+|+++.|+|+|    .+.+.|+|+|.++|.. +++|
T Consensus        78 ~~~~~~~~iG~~v~v~~~~~~~~~~~~~G~L~~~~~~-~i~l  118 (141)
T PF02576_consen   78 SPRDFERFIGRKVKVKLKQPVNGRKEFEGKLLEVDED-EITL  118 (141)
T ss_dssp             SHHHHHHH-SEEEEEE-SS-SSS-SEEEEEEEEEETT-EEEE
T ss_pred             CHHHHHHhcCCeEEEEEeccCCCcEEEEEEEEEEeCC-EEEE
Confidence            35678999999999999    4667999999999983 4555

; PDB: 1IB8_A.

>COG0779 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=87.88  E-value=1.4  Score=38.87  Aligned_cols=38  Identities=21%  Similarity=0.486  Sum_probs=32.8

Q ss_pred             hhhhHHHHhcCCEEEEEE----eCCcEEEEEEEEeccccceEe
Q 023166            4 SKSSKMLQFINYRMRVTI----QDGRQLVGKFMAFDRHMNLVL   42 (286)
Q Consensus         4 ~k~skL~qlIgkRVRVtL----qDGR~fvGtLlAFDKhMNLVL   42 (286)
                      -+.....+|+++.|+|+|    .+.+.|+|+|.++|... |+|
T Consensus        89 ~~~~~f~r~~G~~Vkv~l~~~~~~~k~~~G~i~~~d~~~-v~~  130 (153)
T COG0779          89 KTAEHFARFIGEKVKVKLRLPIEGRKKFEGKIVAVDGET-VTL  130 (153)
T ss_pred             CCHHHHHHhcCcEEEEEEecccCCceEEEEEEEEEcCCe-EEE
Confidence            356778899999999999    89999999999999886 443

>PRK14647 hypothetical protein; Provisional

Probab=87.09  E-value=1.4  Score=38.52  Aligned_cols=38  Identities=8%  Similarity=0.224  Sum_probs=30.4

Q ss_pred             hhhhHHHHhcCCEEEEEEe---------CCcEEEEEEEEeccccceEe
Q 023166            4 SKSSKMLQFINYRMRVTIQ---------DGRQLVGKFMAFDRHMNLVL   42 (286)
Q Consensus         4 ~k~skL~qlIgkRVRVtLq---------DGR~fvGtLlAFDKhMNLVL   42 (286)
                      -+...+.+|+++.|+|+|+         +.+.|+|+|.++|.. +++|
T Consensus        89 ~~~~~f~r~~G~~v~V~l~~~~~~~~~~~~~~~~G~L~~~~~~-~v~l  135 (159)
T PRK14647         89 KKEADYERYAGRLVKVRTFELLADEAGNKRKTFLGELEGLADG-VVTI  135 (159)
T ss_pred             CCHHHHHHhCCcEEEEEEeccccccccCCceEEEEEEEeecCC-EEEE
Confidence            3456789999999999995         369999999999864 3443

>PRK14637 hypothetical protein; Provisional

Probab=86.88  E-value=1.3  Score=38.50  Aligned_cols=38  Identities=24%  Similarity=0.303  Sum_probs=29.9

Q ss_pred             hhhHHHHhcCCEEEEEEeCCcEE-EEEEEEeccccceEeC
Q 023166            5 KSSKMLQFINYRMRVTIQDGRQL-VGKFMAFDRHMNLVLG   43 (286)
Q Consensus         5 k~skL~qlIgkRVRVtLqDGR~f-vGtLlAFDKhMNLVLs   43 (286)
                      +...+.+|+++.|+|+|.+.+.+ +|+|.++|.. +++|.
T Consensus        89 ~~~~f~r~~G~~V~V~l~~~~~~~~G~L~~~~d~-~v~l~  127 (151)
T PRK14637         89 NAAEFSIFVGETVKVWFECTGQWQVGTIAEADET-CLVLT  127 (151)
T ss_pred             CHHHHHHhCCCEEEEEECCCCcEEEEEEEEEeCC-EEEEE
Confidence            45678899999999999545566 7999999876 55554

>PRK14631 hypothetical protein; Provisional

Probab=85.84  E-value=1.7  Score=38.78  Aligned_cols=38  Identities=13%  Similarity=0.349  Sum_probs=31.0

Q ss_pred             hhhhHHHHhcCCEEEEEEe----CCcEEEEEEEEec--cccceEe
Q 023166            4 SKSSKMLQFINYRMRVTIQ----DGRQLVGKFMAFD--RHMNLVL   42 (286)
Q Consensus         4 ~k~skL~qlIgkRVRVtLq----DGR~fvGtLlAFD--KhMNLVL   42 (286)
                      -+...+.+|+++.|+|+|.    +.+.|+|+|.++|  .. +|.|
T Consensus       107 ~~~~df~r~~G~~V~V~l~~~~~~~k~~~G~L~~v~~~~~-~v~l  150 (174)
T PRK14631        107 FQLEQLQGYIGQQVALRLIAAVENRRKFQAKLLAVDLENE-EIQV  150 (174)
T ss_pred             CCHHHHHHhCCCeEEEEEecccCCceEEEEEEEEeecCCC-EEEE
Confidence            3567789999999999995    6699999999998  53 4444

>PRK00092 ribosome maturation protein RimP; Reviewed

Probab=85.44  E-value=1.5  Score=37.73  Aligned_cols=33  Identities=21%  Similarity=0.473  Sum_probs=28.9

Q ss_pred             hhhHHHHhcCCEEEEEE----eCCcEEEEEEEEeccc
Q 023166            5 KSSKMLQFINYRMRVTI----QDGRQLVGKFMAFDRH   37 (286)
Q Consensus         5 k~skL~qlIgkRVRVtL----qDGR~fvGtLlAFDKh   37 (286)
                      +..++.+|+++.|+|+|    .+++.|+|+|..+|..
T Consensus        89 ~~~~f~r~~G~~v~V~~~~~~~~~~~~~G~L~~~~~~  125 (154)
T PRK00092         89 KARDFRRFIGREVKVKLYEPIDGRKKFQGILLAVDGE  125 (154)
T ss_pred             CHHHHHHhCCCeEEEEEEcccCCceEEEEEEEEeeCC
Confidence            45678899999999997    6889999999999874

>PRK06955 biotin--protein ligase; Provisional

Probab=85.29  E-value=2.1  Score=40.50  Aligned_cols=34  Identities=12%  Similarity=0.104  Sum_probs=29.4

Q ss_pred             HHhcCCEEEEEEeCCcEEEEEEEEeccccceEeC
Q 023166           10 LQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLG   43 (286)
Q Consensus        10 ~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLs   43 (286)
                      .-+++++|+|...++++++|+++++|..-.|+|.
T Consensus       245 ~~~~g~~V~v~~~~~~~~~G~~~gId~~G~L~v~  278 (300)
T PRK06955        245 HAYAGREVVLLEDGAELARGVAHGIDETGQLLLD  278 (300)
T ss_pred             hhcCCCeEEEEECCCcEEEEEEeeECCCceEEEE
Confidence            3478899999776778899999999999999985

>PRK14641 hypothetical protein; Provisional

Probab=83.27  E-value=2.5  Score=37.77  Aligned_cols=31  Identities=16%  Similarity=0.291  Sum_probs=26.8

Q ss_pred             hhhHHHHhcCCEEEEEEeC----CcEEEEEEEEec
Q 023166            5 KSSKMLQFINYRMRVTIQD----GRQLVGKFMAFD   35 (286)
Q Consensus         5 k~skL~qlIgkRVRVtLqD----GR~fvGtLlAFD   35 (286)
                      +...+.+|+++.|+|+|.+    .+.|+|+|.++|
T Consensus        95 ~~~~f~r~~G~~V~V~l~~~~~~~~~~~G~L~~~~  129 (173)
T PRK14641         95 LPRQYGRHVGRLLRVTYRDEEGSEHEVTGHLQEVS  129 (173)
T ss_pred             CHHHHHHhCCCEEEEEEecccCCeEEEEEEEEeee
Confidence            4567889999999999975    678999999996

>COG0340 BirA Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]

Probab=83.22  E-value=3  Score=38.68  Aligned_cols=39  Identities=18%  Similarity=0.167  Sum_probs=33.9

Q ss_pred             HHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceE
Q 023166            8 KMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCE   46 (286)
Q Consensus         8 kL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~e   46 (286)
                      +...+++++|+|++.++.++.|+.+++|.+..|+|++.+
T Consensus       184 ~~~~~~g~~V~~~~~~~~~~gg~a~~id~~G~L~l~~~~  222 (238)
T COG0340         184 ARSLSLGKEVRLTLGGGVIFGGIAKGIDEDGALLLETDD  222 (238)
T ss_pred             HHhccCCCEEEEEeCCCcEeeeEEEEECCCceEEEEeCC
Confidence            345579999999999888999999999999999998763

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=81.90  E-value=35  Score=34.60  Aligned_cols=15  Identities=47%  Similarity=0.853  Sum_probs=10.9

Q ss_pred             CCCCCCCCCCCCCCC
Q 023166          189 GPPMARGPPPQGPPQ  203 (286)
Q Consensus       189 ~p~~~~g~ppp~~~~  203 (286)
                      +++|-++++|+..+.
T Consensus       255 pppmpp~PpP~~t~~  269 (498)
T KOG4849|consen  255 PPPMPPAPPPQQTML  269 (498)
T ss_pred             CCCCCCCCCCccccC
Confidence            467888888866655

>PRK14091 RNA-binding protein Hfq; Provisional

Probab=80.78  E-value=2.4  Score=37.97  Aligned_cols=31  Identities=26%  Similarity=0.306  Sum_probs=25.4

Q ss_pred             CEEEEEEeCCcEEEEEEEEeccccceEeCce
Q 023166           15 YRMRVTIQDGRQLVGKFMAFDRHMNLVLGDC   45 (286)
Q Consensus        15 kRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~   45 (286)
                      ..|.|-|.+|-.+.|++++||+|+=|+.+|.
T Consensus       105 ~~VtvfL~NG~~l~G~I~~fD~ftvlL~~~g  135 (165)
T PRK14091        105 EPVTMFLVNGVMLQGEIAAFDLFCMLLERDG  135 (165)
T ss_pred             CcEEEEEecCcEEEEEEEEEcceEEEEEeCC
Confidence            4677778999999999999999986655554

>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional

Probab=80.16  E-value=4.4  Score=38.21  Aligned_cols=32  Identities=19%  Similarity=0.382  Sum_probs=27.6

Q ss_pred             HhcCCEEEEEEeCCcEEEEEEEEeccccceEeC
Q 023166           11 QFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLG   43 (286)
Q Consensus        11 qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLs   43 (286)
                      .++|++|+|.. ++..++|+++++|..-+|+|.
T Consensus       269 ~~~g~~v~~~~-~~~~~~G~~~gi~~~G~L~i~  300 (319)
T PRK11886        269 LFLGREVKLII-GDKEISGIARGIDEQGALLLE  300 (319)
T ss_pred             cccCCeEEEEe-CCcEEEEEEEEECCCceEEEE
Confidence            47889999987 456799999999999999985

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	286
2y9a_A	95	Structure Of The Spliceosomal U4 Snrnp Core Domain		7e-30
1d3b_B	91	Crystal Structure Of The D3b Subcomplex Of The Huma		9e-30
3pgw_B	231	Crystal Structure Of Human U1 Snrnp Length = 231		1e-29
3cw1_A	174	Crystal Structure Of Human Spliceosomal U1 Snrnp Le		2e-29
3swn_C	117	Structure Of The Lsm657 Complex: An Assembly Interm		2e-04

>pdb|2Y9A|A Chain A, Structure Of The Spliceosomal U4 Snrnp Core Domain Length = 95

Iteration: 1
 Score =  127 bits (319), Expect = 7e-30,   Method: Compositional matrix adjust.
 Identities = 58/93 (62%), Positives = 73/93 (78%), Gaps = 4/93 (4%)
Query: 1  MSMSKSSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNN 60
          M++ KSSKMLQ I+YRMR  +QDGR  +G F AFD+HMNL+L DC+EFRK+ P    KN+
Sbjct: 1  MTVGKSSKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKP----KNS 56
Query: 61 TNEEREDRRTLGLVLLRGEEVISMTVEGPPPPE 93
             ERE++R LGLVLLRGE ++SMTVEGPPP +
Sbjct: 57 KQAEREEKRVLGLVLLRGENLVSMTVEGPPPKD 89

>pdb|1D3B|B Chain B, Crystal Structure Of The D3b Subcomplex Of The Human Core Snrnp Domain At 2.0a Resolution Length = 91

Iteration: 1
 Score =  127 bits (318), Expect = 9e-30,   Method: Compositional matrix adjust.
 Identities = 58/93 (62%), Positives = 73/93 (78%), Gaps = 4/93 (4%)
Query: 1  MSMSKSSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNN 60
          M++ KSSKMLQ I+YRMR  +QDGR  +G F AFD+HMNL+L DC+EFRK+ P    KN+
Sbjct: 1  MTVGKSSKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKP----KNS 56
Query: 61 TNEEREDRRTLGLVLLRGEEVISMTVEGPPPPE 93
             ERE++R LGLVLLRGE ++SMTVEGPPP +
Sbjct: 57 KQAEREEKRVLGLVLLRGENLVSMTVEGPPPKD 89

>pdb|3PGW|B Chain B, Crystal Structure Of Human U1 Snrnp Length = 231

Iteration: 1
 Score =  126 bits (316), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 58/93 (62%), Positives = 73/93 (78%), Gaps = 4/93 (4%)
Query: 1  MSMSKSSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNN 60
          M++ KSSKMLQ I+YRMR  +QDGR  +G F AFD+HMNL+L DC+EFRK+ P    KN+
Sbjct: 1  MTVGKSSKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKP----KNS 56
Query: 61 TNEEREDRRTLGLVLLRGEEVISMTVEGPPPPE 93
             ERE++R LGLVLLRGE ++SMTVEGPPP +
Sbjct: 57 KQAEREEKRVLGLVLLRGENLVSMTVEGPPPKD 89

>pdb|3CW1|A Chain A, Crystal Structure Of Human Spliceosomal U1 Snrnp Length = 174

Iteration: 1
 Score =  125 bits (315), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 58/93 (62%), Positives = 73/93 (78%), Gaps = 4/93 (4%)
Query: 1  MSMSKSSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNN 60
          M++ KSSKMLQ I+YRMR  +QDGR  +G F AFD+HMNL+L DC+EFRK+ P    KN+
Sbjct: 1  MTVGKSSKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKP----KNS 56
Query: 61 TNEEREDRRTLGLVLLRGEEVISMTVEGPPPPE 93
             ERE++R LGLVLLRGE ++SMTVEGPPP +
Sbjct: 57 KQAEREEKRVLGLVLLRGENLVSMTVEGPPPKD 89

>pdb|3SWN|C Chain C, Structure Of The Lsm657 Complex: An Assembly Intermediate Of The Lsm1 7 And Lsm2 8 Rings Length = 117

Iteration: 1
 Score = 42.7 bits (99), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 26/72 (36%), Positives = 38/72 (52%), Gaps = 7/72 (9%)
Query: 11 QFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRT 70
          ++ + R++ T   GRQ+ G    FD+ MNLVL D EE  +  P  GK           R 
Sbjct: 34 RYQDQRIQATFTGGRQITGILKGFDQLMNLVLDDVEEQLR-NPEDGKLTGA------IRK 86
Query: 71 LGLVLLRGEEVI 82
          LGLV++RG  ++
Sbjct: 87 LGLVVVRGTTLV 98

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	286
1d3b_B	91	Protein (small nuclear ribonucleoprotein associat	2e-35
3bw1_A	96	SMX4 protein, U6 snRNA-associated SM-like protein	1e-21
2fwk_A	121	U6 snRNA-associated SM-like protein LSM5; structur	1e-20
4emg_A	93	Probable U6 snRNA-associated SM-like protein LSM3;	1e-19
1b34_B	118	Protein (small nuclear ribonucleoprotein SM D2); s	4e-19
3s6n_G	76	Small nuclear ribonucleoprotein G; SMN complex, SM	2e-18
3pgw_B	231	SM B; protein-RNA complex, U1 snRNA, SM fold, SM c	2e-18
1th7_A	81	SnRNP-2, small nuclear riboprotein protein; archae	3e-17
1mgq_A	83	SM-like protein; LSM, RNA-binding, archea, RNA bin	2e-16
1h64_1	75	SnRNP SM-like protein; SM fold, spliceosome, snRNP	9e-16
4emk_C	113	U6 snRNA-associated SM-like protein LSM7; SM fold,	5e-15
1i4k_A	77	Putative snRNP SM-like protein; core snRNP domain,	1e-14
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	2e-14
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	8e-14
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	1e-13
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	3e-10
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	1e-09
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	1e-07
1i8f_A	81	Putative snRNP SM-like protein; beta barrel-like S	1e-13
3s6n_E	92	Small nuclear ribonucleoprotein E; SMN complex, SM	5e-13
4emk_B	75	U6 snRNA-associated SM-like protein LSM6; SM fold,	2e-12
4emk_A	94	U6 snRNA-associated SM-like protein LSM5; SM fold,	4e-11
3s6n_F	86	Small nuclear ribonucleoprotein F; SMN complex, SM	6e-11
1ljo_A	77	Archaeal SM-like protein AF-SM2; snRNP, core snRNP	1e-10
1n9r_A	93	SMF, small nuclear ribonucleoprotein F, snRNP-F, S	1e-06
3v1v_A	433	2-MIB synthase, 2-methylisoborneol synthase; class	7e-06
3v1v_A	433	2-MIB synthase, 2-methylisoborneol synthase; class	1e-05
3v1v_A	433	2-MIB synthase, 2-methylisoborneol synthase; class	2e-05
3v1v_A	433	2-MIB synthase, 2-methylisoborneol synthase; class	3e-05
3v1v_A	433	2-MIB synthase, 2-methylisoborneol synthase; class	1e-04
3h0g_A	1752	DNA-directed RNA polymerase II subunit RPB1; trans	1e-05
3dzy_A	467	Retinoic acid receptor RXR-alpha; DNA-binding, HOS	3e-05
3dzy_A	467	Retinoic acid receptor RXR-alpha; DNA-binding, HOS	2e-04
2z73_A	448	Rhodopsin; visual pigment, GQ-type, G-protein coup	5e-05
2z73_A	448	Rhodopsin; visual pigment, GQ-type, G-protein coup	4e-04
2z73_A	448	Rhodopsin; visual pigment, GQ-type, G-protein coup	5e-04
1twf_A	1733	B220, DNA-directed RNA polymerase II largest subun	6e-05
1twf_A	1733	B220, DNA-directed RNA polymerase II largest subun	2e-04
1twf_A	1733	B220, DNA-directed RNA polymerase II largest subun	2e-04
3tx7_B	352	Nuclear receptor subfamily 5 group A member 2; LRH	4e-04
3lvg_A	624	Clathrin heavy chain 1; SELF assembly, coated PIT,	4e-04
3lvg_A	624	Clathrin heavy chain 1; SELF assembly, coated PIT,	8e-04
4emh_A	105	Probable U6 snRNA-associated SM-like protein LSM4;	4e-04
2z6g_A	780	B-catenin; FULL-length, beta-catenin, cell adhesio	6e-04

>1d3b_B Protein (small nuclear ribonucleoprotein associat B); snRNP, splicing, core snRNP domain, systemic lupus eryth SLE, RNA binding protein; HET: CIT; 2.00A {Homo sapiens} SCOP: b.38.1.1 PDB: 2y9a_A 2y9b_A 2y9c_A 2y9d_A Length = 91

 Score =  121 bits (306), Expect = 2e-35
 Identities = 58/94 (61%), Positives = 73/94 (77%), Gaps = 4/94 (4%)

Query: 1  MSMSKSSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNN 60
          M++ KSSKMLQ I+YRMR  +QDGR  +G F AFD+HMNL+L DC+EFRK+ P    KN+
Sbjct: 1  MTVGKSSKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKP----KNS 56

Query: 61 TNEEREDRRTLGLVLLRGEEVISMTVEGPPPPEE 94
             ERE++R LGLVLLRGE ++SMTVEGPPP + 
Sbjct: 57 KQAEREEKRVLGLVLLRGENLVSMTVEGPPPKDT 90

>3bw1_A SMX4 protein, U6 snRNA-associated SM-like protein LSM3; RNA-binding protein, SM protein, ring, HOMO octamer, mRNA processing; 2.50A {Saccharomyces cerevisiae} Length = 96

 Score = 85.9 bits (213), Expect = 1e-21
 Identities = 23/84 (27%), Positives = 36/84 (42%), Gaps = 10/84 (11%)

Query: 11 QFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRT 70
            ++ R+ + ++  R LVG   AFD H N+VL D  E            N  E  E  R 
Sbjct: 17 LNLDERVYIKLRGARTLVGTLQAFDSHCNIVLSDAVETIYQL-------NNEELSESERR 69

Query: 71 LGLVLLRGEEVISMTVEGPPPPEE 94
            +V +RG+ V  +     P  ++
Sbjct: 70 CEMVFIRGDTVTLI---STPSEDD 90

>2fwk_A U6 snRNA-associated SM-like protein LSM5; structural genomics, structural genomics consortium, SGC, DNA binding protein; 2.14A {Cryptosporidium parvum} SCOP: b.38.1.1 PDB: 3pgg_A Length = 121

 Score = 83.9 bits (207), Expect = 1e-20
 Identities = 19/83 (22%), Positives = 35/83 (42%), Gaps = 1/83 (1%)

Query: 11  QFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNE-EREDRR 69
           + I  R+ V ++  ++  G    FD ++N+VL D +E+      +       + +R    
Sbjct: 35  KCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGGNKKLKRVMVN 94

Query: 70  TLGLVLLRGEEVISMTVEGPPPP 92
            L  +LL G  V  +   G P  
Sbjct: 95  RLETILLSGNNVAMLVPGGDPDS 117

>4emg_A Probable U6 snRNA-associated SM-like protein LSM3; SM fold, mRNA decay, LSM proteins, RNA binding protein; 2.70A {Schizosaccharomyces pombe} Length = 93

 Score = 80.7 bits (199), Expect = 1e-19
 Identities = 21/81 (25%), Positives = 41/81 (50%), Gaps = 4/81 (4%)

Query: 11 QFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRT 70
            ++  + V ++  R+L G+  A+D H+N+VLGD EE   +     + +     +  R+ 
Sbjct: 16 LSLDEIVYVKLRGDRELNGRLHAYDEHLNMVLGDAEEIVTIFD-DEETDKDKALKTIRKH 74

Query: 71 LGLVLLRGEEVISMTVEGPPP 91
            ++ +RG+ VI +    PP 
Sbjct: 75 YEMLFVRGDSVILIA---PPR 92

>1b34_B Protein (small nuclear ribonucleoprotein SM D2); snRNP, splicing, spliceosome, core snRNP domain, systemi erythematosus, SLE, RNA binding protein; 2.50A {Homo sapiens} SCOP: b.38.1.1 PDB: 2y9a_C 2y9b_C 2y9c_C 2y9d_C 3cw1_C 3pgw_Y* 3s6n_B Length = 118

 Score = 80.0 bits (197), Expect = 4e-19
 Identities = 22/83 (26%), Positives = 41/83 (49%), Gaps = 3/83 (3%)

Query: 14  NYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGL 73
           N ++ +  ++ ++L+G+  AFDRH N+VL + +E     P  GK    ++     R +  
Sbjct: 39  NTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKGKKKSKPVNKDRYISK 98

Query: 74  VLLRGEEVISMTVEGPPPPEESR 96
           + LRG+ VI +      P    +
Sbjct: 99  MFLRGDSVIVVL---RNPLIAGK 118

>3s6n_G Small nuclear ribonucleoprotein G; SMN complex, SMN-gemin2 complex, U-rich snRNA, SM fold, SM C SNRNPS, snRNP biogenesis, PRE-mRNA splicing; 2.50A {Homo sapiens} PDB: 2y9b_G 2y9c_G 2y9d_G 3cw1_G 3pgw_G* 2y9a_G Length = 76

 Score = 76.6 bits (189), Expect = 2e-18
 Identities = 19/84 (22%), Positives = 39/84 (46%), Gaps = 14/84 (16%)

Query: 1  MSMSKSSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNN 60
          MS +   ++ +F++ ++ + +  GR + G    FD  MNLV+ +C E             
Sbjct: 1  MSKAHPPELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMAT---------- 50

Query: 61 TNEEREDRRTLGLVLLRGEEVISM 84
                 +  +G+V++RG  +I +
Sbjct: 51 ----SGQQNNIGMVVIRGNSIIML 70

>3pgw_B SM B; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_A Length = 231

 Score = 80.8 bits (199), Expect = 2e-18
 Identities = 114/237 (48%), Positives = 139/237 (58%), Gaps = 9/237 (3%)

Query: 1   MSMSKSSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNN 60
           M++ KSSKMLQ I+YRMR  +QDGR  +G F AFD+HMNL+L DC+EFRK+ P    KN+
Sbjct: 1   MTVGKSSKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKP----KNS 56

Query: 61  TNEEREDRRTLGLVLLRGEEVISMTVEGPPPPEESRAKAVSASAVAGPGIGRAAGRGVPA 120
              ERE++R LGLVLLRGE ++SMTVEGPPP +   A+   A A  GPGIGRAAGRG+PA
Sbjct: 57  KQAEREEKRVLGLVLLRGENLVSMTVEGPPPKDTGIARVPLAGAAGGPGIGRAAGRGIPA 116

Query: 121 A-PLVQAQPGLAGPVRGVGGPAPGMMQPQISRPPIPQLSAPPMTYPATSGGPPVIRPPGQ 179
             P+ QA  GLAGPVRGVGGP+  +M PQ         +A   +      G P   PPG+
Sbjct: 117 GVPMPQAPAGLAGPVRGVGGPSQQVMTPQGRGTVAAAAAAATASIA----GAPTQYPPGR 172

Query: 180 MPPPVYPGQGPPMARGPPPQGPPQGFGVRPPQQFPMPPQQFGQRPMVPPPPGPMMRG 236
             PP   G+G P      P    +     P    P      G  P    PP P MRG
Sbjct: 173 GGPPPPMGRGAPPPGMMGPPPGMRPPMGPPMGIPPGRGTPMGMPPPGMRPPPPGMRG 229

>1th7_A SnRNP-2, small nuclear riboprotein protein; archaea, SM protein, SM fold, SS-SM1, RNA binding protein; 1.68A {Sulfolobus solfataricus} SCOP: b.38.1.1 Length = 81

 Score = 73.9 bits (182), Expect = 3e-17
 Identities = 22/88 (25%), Positives = 46/88 (52%), Gaps = 17/88 (19%)

Query: 1  MS-MSK-SSKMLQ-FINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGK 57
          M+ +++ + K+L   +N  + V ++  +++ G   ++D+HMNLVL D EE          
Sbjct: 3  MNFLAETAHKVLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEI--------- 53

Query: 58 KNNTNEEREDRRTLGLVLLRGEEVISMT 85
               +     + LG +++RG+ VI ++
Sbjct: 54 -----QSDGSGKKLGTIVIRGDNVILIS 76

>1mgq_A SM-like protein; LSM, RNA-binding, archea, RNA binding protein; 1.70A {Methanothermobacterthermautotrophicus} SCOP: b.38.1.1 PDB: 1i81_A 1loj_A* 1jbm_A 1jri_A Length = 83

 Score = 71.6 bits (176), Expect = 2e-16
 Identities = 24/86 (27%), Positives = 42/86 (48%), Gaps = 15/86 (17%)

Query: 1  MSMSKSSKMLQ-FINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKN 59
          +++ +    L   +N  + + ++  R+  G   +FD HMNLVL D EE            
Sbjct: 11 VNVQRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEEL----------- 59

Query: 60 NTNEEREDRRTLGLVLLRGEEVISMT 85
             E+ E  R LG VL+RG+ ++ ++
Sbjct: 60 ---EDGEVTRRLGTVLIRGDNIVYIS 82

>1h64_1 SnRNP SM-like protein; SM fold, spliceosome, snRNP core; 1.9A {Pyrococcus abyssi} SCOP: b.38.1.1 PDB: 1m8v_A* Length = 75

 Score = 69.6 bits (171), Expect = 9e-16
 Identities = 19/94 (20%), Positives = 45/94 (47%), Gaps = 21/94 (22%)

Query: 3  MSKS-SKMLQ-FINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNN 60
          M++    ++   ++  + V ++ G +  G+ + +D H+N+VL D E              
Sbjct: 1  MAERPLDVIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMI------------ 48

Query: 61 TNEEREDRRTLGLVLLRGEEVISMTVEGPPPPEE 94
            ++ E  +  G +++RG+ V++++     P EE
Sbjct: 49 --QDGEVVKRYGKIVIRGDNVLAIS-----PTEE 75

>4emk_C U6 snRNA-associated SM-like protein LSM7; SM fold, mRNA decay and PRE-mRNA splicing, LSM proteins, RNA protein; 2.30A {Schizosaccharomyces pombe} PDB: 3swn_C Length = 113

 Score = 68.8 bits (168), Expect = 5e-15
 Identities = 24/74 (32%), Positives = 38/74 (51%), Gaps = 7/74 (9%)

Query: 11 QFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRT 70
          ++ + R++ T   GRQ+ G    FD+ MNLVL D EE  + P          +     R 
Sbjct: 30 RYQDQRIQATFTGGRQITGILKGFDQLMNLVLDDVEEQLRNP-------EDGKLTGAIRK 82

Query: 71 LGLVLLRGEEVISM 84
          LGLV++RG  ++ +
Sbjct: 83 LGLVVVRGTTLVLI 96

>1i4k_A Putative snRNP SM-like protein; core snRNP domain, RNA binding protein; HET: CIT; 2.50A {Archaeoglobus fulgidus} SCOP: b.38.1.1 PDB: 1i5l_A* Length = 77

 Score = 66.5 bits (163), Expect = 1e-14
 Identities = 25/94 (26%), Positives = 41/94 (43%), Gaps = 17/94 (18%)

Query: 1  MSMSKSSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNN 60
          M       + + +   + V ++ GR+  G    +D HMNLVL D EE             
Sbjct: 1  MPPRPLDVLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEI------------ 48

Query: 61 TNEEREDRRTLGLVLLRGEEVISMTVEGPPPPEE 94
            +  E  R +G V++RG+ V+ ++   P P  E
Sbjct: 49 --QNGEVVRKVGSVVIRGDTVVFVS---PAPGGE 77

>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein, abnormal nuclear; zinc-finger, beta barrel, VWA domain, gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1 Length = 926

 Score = 72.6 bits (177), Expect = 2e-14
 Identities = 21/129 (16%), Positives = 28/129 (21%)

Query: 158 SAPPMTYPATSGGPPVIRPPGQMPPPVYPGQGPPMARGPPPQGPPQGFGVRPPQQFPMPP 217
                 YP           P Q P    P Q P  A     Q      G  P        
Sbjct: 3   HHKKRVYPQAQLQYGQNATPLQQPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQFL 62

Query: 218 QQFGQRPMVPPPPGPMMRGPPSGPPRPGMPNAPPPRPGMPPPPGAPVFRPGMPPPPPNAQ 277
               ++                    P +      +P +P   G P+ +   P   P   
Sbjct: 63  TPAQEQLHQQIDQATTSMNDMHLHNVPLVDPNAYMQPQVPVQMGTPLQQQQQPMAAPAYG 122

Query: 278 QQQQNQQQQ 286
           Q      Q 
Sbjct: 123 QPSAAMGQN 131

>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein, abnormal nuclear; zinc-finger, beta barrel, VWA domain, gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1 Length = 926

 Score = 70.6 bits (172), Expect = 8e-14
 Identities = 25/147 (17%), Positives = 30/147 (20%), Gaps = 4/147 (2%)

Query: 144 MMQPQISRPPIPQLSAPPMTYPATSGGPPVIRPPGQMPPPVYPGQGPPMARGPPPQGPPQ 203
           M   +    P  QL       P       +           Y   G P     P  G  Q
Sbjct: 1   MSHHKKRVYPQAQLQYGQNATPLQQPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQ 60

Query: 204 GFGVRPPQQ----FPMPPQQFGQRPMVPPPPGPMMRGPPSGPPRPGMPNAPPPRPGMPPP 259
                  Q                    P   P     P  P + G P     +P   P 
Sbjct: 61  FLTPAQEQLHQQIDQATTSMNDMHLHNVPLVDPNAYMQPQVPVQMGTPLQQQQQPMAAPA 120

Query: 260 PGAPVFRPGMPPPPPNAQQQQQNQQQQ 286
            G P    G    P N         + 
Sbjct: 121 YGQPSAAMGQNMRPMNQLYPIDLLTEL 147

>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein, abnormal nuclear; zinc-finger, beta barrel, VWA domain, gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1 Length = 926

 Score = 69.9 bits (170), Expect = 1e-13
 Identities = 26/165 (15%), Positives = 37/165 (22%), Gaps = 2/165 (1%)

Query: 122 PLVQAQPGLAGPVRGVGGPAPGMMQPQISRPPIPQLSAPPMTYPATSGGPPVIRPPGQMP 181
           P  Q Q G                 P  +     Q+  PP     + G    + P  +  
Sbjct: 10  PQAQLQYGQNATPLQQPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQFLTPAQEQL 69

Query: 182 PPVYPGQGPPMARGPPPQGPPQGFGVRPPQQFP--MPPQQFGQRPMVPPPPGPMMRGPPS 239
                     M        P          Q P  M      Q+  +  P          
Sbjct: 70  HQQIDQATTSMNDMHLHNVPLVDPNAYMQPQVPVQMGTPLQQQQQPMAAPAYGQPSAAMG 129

Query: 240 GPPRPGMPNAPPPRPGMPPPPGAPVFRPGMPPPPPNAQQQQQNQQ 284
              RP     P       PPP   +  P  P   P  +    ++ 
Sbjct: 130 QNMRPMNQLYPIDLLTELPPPITDLTLPPPPLVIPPERMLVPSEL 174

>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein, abnormal nuclear; zinc-finger, beta barrel, VWA domain, gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1 Length = 926

 Score = 59.5 bits (143), Expect = 3e-10
 Identities = 25/154 (16%), Positives = 31/154 (20%)

Query: 106 AGPGIGRAAGRGVPAAPLVQAQPGLAGPVRGVGGPAPGMMQPQISRPPIPQLSAPPMTYP 165
                 +   + +P      A            G  P M Q Q   P   QL        
Sbjct: 18  QNATPLQQPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQFLTPAQEQLHQQIDQAT 77

Query: 166 ATSGGPPVIRPPGQMPPPVYPGQGPPMARGPPPQGPPQGFGVRPPQQFPMPPQQFGQRPM 225
            +     +   P   P      Q P     P  Q           Q      Q       
Sbjct: 78  TSMNDMHLHNVPLVDPNAYMQPQVPVQMGTPLQQQQQPMAAPAYGQPSAAMGQNMRPMNQ 137

Query: 226 VPPPPGPMMRGPPSGPPRPGMPNAPPPRPGMPPP 259
           + P        PP        P    P   M  P
Sbjct: 138 LYPIDLLTELPPPITDLTLPPPPLVIPPERMLVP 171

>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein, abnormal nuclear; zinc-finger, beta barrel, VWA domain, gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1 Length = 926

 Score = 58.3 bits (140), Expect = 1e-09
 Identities = 31/170 (18%), Positives = 41/170 (24%), Gaps = 6/170 (3%)

Query: 113 AAGRGVPAAPLVQAQPGLAGPVRGVGGPAPGMMQPQISRPPIPQLSAPPMTYPATSGGPP 172
           A     PA  +    P  AG   G  G  P    P + +       A    +        
Sbjct: 20  ATPLQQPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQFLT-PAQEQLHQQIDQATT 78

Query: 173 VIRPPGQMPPPVYPGQGPPMARGPPPQGPPQGFGVRPPQQFPMPPQQFGQRPMVPPPPGP 232
            +        P+         + P   G P        QQ PM    +GQ          
Sbjct: 79  SMNDMHLHNVPLVDPNAYMQPQVPVQMGTPL-----QQQQQPMAAPAYGQPSAAMGQNMR 133

Query: 233 MMRGPPSGPPRPGMPNAPPPRPGMPPPPGAPVFRPGMPPPPPNAQQQQQN 282
            M           +P         PPP   P  R  +P    NA      
Sbjct: 134 PMNQLYPIDLLTELPPPITDLTLPPPPLVIPPERMLVPSELSNASPDYIR 183

>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein, abnormal nuclear; zinc-finger, beta barrel, VWA domain, gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1 Length = 926

 Score = 51.4 bits (122), Expect = 1e-07
 Identities = 32/165 (19%), Positives = 43/165 (26%), Gaps = 10/165 (6%)

Query: 88  GPPPPEESRAKAVSASAVAGPGIGRAAGRGVPAAPLVQAQPGLAGPVRGVGGPAPGMMQP 147
             P  + ++       A AG   G+       A P +  Q  L      +          
Sbjct: 20  ATPLQQPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQFLTPAQEQLHQQIDQATTS 79

Query: 148 QISRPPIPQLSAPPMTYPATSGGPPVIRPPGQMPPPVYPGQGPPMARGPPPQGPPQGFGV 207
                    L   P+  P     P     P QM  P+   Q P  A          G  +
Sbjct: 80  ----MNDMHLHNVPLVDPNAYMQPQ---VPVQMGTPLQQQQQPMAAPAYGQPSAAMGQNM 132

Query: 208 RPPQQFPMPPQQFGQRPMVPPPPGPMMRGPPSGPPRPGMPNAPPP 252
           RP  Q   P     + P  PP     +  PP   P   M      
Sbjct: 133 RPMNQ-LYPIDLLTELP--PPITDLTLPPPPLVIPPERMLVPSEL 174

>1i8f_A Putative snRNP SM-like protein; beta barrel-like SMAP monomers form 35-stranded beta-sheet I heptamer, structural genomics; 1.75A {Pyrobaculum aerophilum} SCOP: b.38.1.1 PDB: 1lnx_A* Length = 81

 Score = 64.3 bits (157), Expect = 1e-13
 Identities = 22/89 (24%), Positives = 40/89 (44%), Gaps = 17/89 (19%)

Query: 2  SMSKSSKMLQ-FINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNN 60
            +     LQ  I  ++ V ++D  ++ G   +FD+H+NL+L D EE             
Sbjct: 8  CFATLGATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIID---------- 57

Query: 61 TNEEREDRRTLGLVLLRGEEVISMT-VEG 88
                +    G +++RGE V+ ++ V G
Sbjct: 58 -----GNVYKRGTMVVRGENVLFISPVPG 81

>3s6n_E Small nuclear ribonucleoprotein E; SMN complex, SMN-gemin2 complex, U-rich snRNA, SM fold, SM C SNRNPS, snRNP biogenesis, PRE-mRNA splicing; 2.50A {Homo sapiens} PDB: 2y9b_E 2y9c_E 2y9d_E 3cw1_E 3pgw_E* 2y9a_E Length = 92

 Score = 62.9 bits (153), Expect = 5e-13
 Identities = 19/81 (23%), Positives = 39/81 (48%), Gaps = 17/81 (20%)

Query: 9  MLQFINYRMRVTI----QDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEE 64
          + +++  R R+ +    Q   ++ G  + FD +MNLVL D EE              + +
Sbjct: 21 IFRYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEI-------------HSK 67

Query: 65 REDRRTLGLVLLRGEEVISMT 85
           + R+ LG ++L+G+ +  + 
Sbjct: 68 TKSRKQLGRIMLKGDNITLLQ 88

>4emk_B U6 snRNA-associated SM-like protein LSM6; SM fold, mRNA decay and PRE-mRNA splicing, LSM proteins, RNA protein; 2.30A {Schizosaccharomyces pombe} PDB: 3swn_B Length = 75

 Score = 60.8 bits (148), Expect = 2e-12
 Identities = 16/94 (17%), Positives = 32/94 (34%), Gaps = 19/94 (20%)

Query: 1  MSMSKSSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNN 60
          M  S +  + + I  ++ + +  G    G     D +MNL L   EE+            
Sbjct: 1  MDSSPNEFLNKVIGKKVLIRLSSGVDYKGILSCLDGYMNLALERTEEY------------ 48

Query: 61 TNEEREDRRTLGLVLLRGEEVISMTVEGPPPPEE 94
               +     G   +RG  V+ ++       ++
Sbjct: 49 --VNGKKTNVYGDAFIRGNNVLYVS-----ALDD 75

>4emk_A U6 snRNA-associated SM-like protein LSM5; SM fold, mRNA decay and PRE-mRNA splicing, LSM proteins, RNA protein; 2.30A {Schizosaccharomyces pombe} PDB: 3swn_A Length = 94

 Score = 57.5 bits (139), Expect = 4e-11
 Identities = 16/80 (20%), Positives = 30/80 (37%), Gaps = 13/80 (16%)

Query: 11 QFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRT 70
          + I   + V ++  R+  G  + FD ++N+VL D  E+             +        
Sbjct: 27 KCIGSNLWVIMKSEREFAGTLVGFDDYVNIVLKDVTEY-------------DTVTGVTEK 73

Query: 71 LGLVLLRGEEVISMTVEGPP 90
             +LL G  +  +   G P
Sbjct: 74 HSEMLLNGNGMCMLIPGGKP 93

>3s6n_F Small nuclear ribonucleoprotein F; SMN complex, SMN-gemin2 complex, U-rich snRNA, SM fold, SM C SNRNPS, snRNP biogenesis, PRE-mRNA splicing; 2.50A {Homo sapiens} PDB: 2y9b_F 2y9c_F 2y9d_F 3cw1_F 3pgw_F* 2y9a_F Length = 86

 Score = 56.7 bits (137), Expect = 6e-11
 Identities = 21/96 (21%), Positives = 37/96 (38%), Gaps = 18/96 (18%)

Query: 1  MSMSKS-SKMLQ-FINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKK 58
          MS+  +    L       + V ++ G +  G  ++ D +MN+ L + EE+          
Sbjct: 1  MSLPLNPKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEY---------- 50

Query: 59 NNTNEEREDRRTLGLVLLRGEEVISMTVEGPPPPEE 94
               +      LG VL+R   V  + + G    EE
Sbjct: 51 ----IDGALSGHLGEVLIRCNNV--LYIRGVEEEEE 80

>1ljo_A Archaeal SM-like protein AF-SM2; snRNP, core snRNP domain, RNA binding protein, unknown F; 1.95A {Archaeoglobus fulgidus} SCOP: b.38.1.1 Length = 77

 Score = 55.8 bits (135), Expect = 1e-10
 Identities = 24/85 (28%), Positives = 37/85 (43%), Gaps = 20/85 (23%)

Query: 11 QFINYRMRVTIQ-DGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRR 69
            +   +RV ++ +  QLVGK    D +MNL L +  E               +  E  R
Sbjct: 12 SMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMEC--------------KGEEKVR 57

Query: 70 TLGLVLLRGEEVISMTVEGPPPPEE 94
          +LG ++LRG  V+ +      P EE
Sbjct: 58 SLGEIVLRGNNVVLIQ-----PQEE 77

>1n9r_A SMF, small nuclear ribonucleoprotein F, snRNP-F, SM protein F; heptamer, translation; 2.80A {Saccharomyces cerevisiae} SCOP: b.38.1.1 PDB: 1n9s_A Length = 93

 Score = 45.2 bits (107), Expect = 1e-06
 Identities = 22/103 (21%), Positives = 38/103 (36%), Gaps = 29/103 (28%)

Query: 1  MSMSKSSKMLQF------------INYRMRVTIQD-GRQLVGKFMAFDRHMNLVLGDCEE 47
            MS+SS +               +N+R+ V ++    +  G  ++ D + NL L + EE
Sbjct: 6  HHMSESSDISAMQPVNPKPFLKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEE 65

Query: 48 FRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMTVEGPP 90
          F       G             TLG + +R   V  + +   P
Sbjct: 66 F-----VAGVS---------HGTLGEIFIRCNNV--LYIRELP 92

>3v1v_A 2-MIB synthase, 2-methylisoborneol synthase; class I terpenoid cyclase fold, DDXXXXD motif, NDXXSXXXE MOT methylisoborneol biosynthesis; HET: GST; 1.80A {Streptomyces coelicolor} PDB: 3v1x_A* Length = 433

 Score = 45.9 bits (108), Expect = 7e-06
 Identities = 27/141 (19%), Positives = 36/141 (25%), Gaps = 16/141 (11%)

Query: 140 PAPGMMQPQISRPPIPQLSAPPMTYPATSGGPPVIRPPGQMPPPVYPGQGPPMARGPPPQ 199
                + P+ S   IP  S       A S     + PP  +P P  P    P A  PP  
Sbjct: 9   HHSSGLVPRGSHMVIPSASVTS----AASDFLAALHPPVTVPDPAPPPPPAPAAGNPPDT 64

Query: 200 GPPQGFGVRPPQQFPMPPQQFGQRPMVPPPPGPMMRGPPSGPPRPGMPNAPPPRPG-MPP 258
                             Q+  + P  P              P P  P + PP  G   P
Sbjct: 65  VTG-----------DSVLQRILRGPTGPGTTSLAPAVRYGRQPGPEAPASAPPAAGRAVP 113

Query: 259 PPGAPVFRPGMPPPPPNAQQQ 279
                      P       ++
Sbjct: 114 GLYHHPVPEPDPVRVEEVSRR 134

>3v1v_A 2-MIB synthase, 2-methylisoborneol synthase; class I terpenoid cyclase fold, DDXXXXD motif, NDXXSXXXE MOT methylisoborneol biosynthesis; HET: GST; 1.80A {Streptomyces coelicolor} PDB: 3v1x_A* Length = 433

 Score = 45.1 bits (106), Expect = 1e-05
 Identities = 13/104 (12%), Positives = 16/104 (15%)

Query: 171 PPVIRPPGQMPPPVYPGQGPPMARGPPPQGPPQGFGVRPPQQFPMPPQQFGQRPMVPPPP 230
                    + P       P  +                    P PP         PP  
Sbjct: 5   HHHHHHSSGLVPRGSHMVIPSASVTSAASDFLAALHPPVTVPDPAPPPPPAPAAGNPPDT 64

Query: 231 GPMMRGPPSGPPRPGMPNAPPPRPGMPPPPGAPVFRPGMPPPPP 274
                        P  P      P +          P   PP  
Sbjct: 65  VTGDSVLQRILRGPTGPGTTSLAPAVRYGRQPGPEAPASAPPAA 108

>3v1v_A 2-MIB synthase, 2-methylisoborneol synthase; class I terpenoid cyclase fold, DDXXXXD motif, NDXXSXXXE MOT methylisoborneol biosynthesis; HET: GST; 1.80A {Streptomyces coelicolor} PDB: 3v1x_A* Length = 433

 Score = 44.7 bits (105), Expect = 2e-05
 Identities = 21/124 (16%), Positives = 33/124 (26%), Gaps = 2/124 (1%)

Query: 139 GPAPGMMQPQISRPPIPQLSAPPMTYPATSGGPPVIRPPGQMPPPVYPGQGPPMARGPPP 198
             +  + +      P   +++    + A    P  +  P   PPP      PP       
Sbjct: 10  HSSGLVPRGSHMVIPSASVTSAASDFLAALHPPVTVPDPAPPPPPAPAAGNPPDTVTGDS 69

Query: 199 QGPPQGFGVRPPQQFPMPPQQFGQRPMVPPPPGPMMRGPPSGPPRPGMPNAPPPRPGMPP 258
                  G  P            +    P P  P    P +G   PG+ + P P P    
Sbjct: 70  VLQRILRG--PTGPGTTSLAPAVRYGRQPGPEAPASAPPAAGRAVPGLYHHPVPEPDPVR 127

Query: 259 PPGA 262
               
Sbjct: 128 VEEV 131

>3v1v_A 2-MIB synthase, 2-methylisoborneol synthase; class I terpenoid cyclase fold, DDXXXXD motif, NDXXSXXXE MOT methylisoborneol biosynthesis; HET: GST; 1.80A {Streptomyces coelicolor} PDB: 3v1x_A* Length = 433

 Score = 44.0 bits (103), Expect = 3e-05
 Identities = 12/109 (11%), Positives = 17/109 (15%), Gaps = 7/109 (6%)

Query: 177 PGQMPPPVYPGQGPPMARGPPPQGPPQGFGVRPPQQFPMPPQQFGQRPMVPPPPGPMMRG 236
                              P                F          P  P PP P    
Sbjct: 5   HHHHHHSSGLVPRGSHMVIPSASVTS------AASDFLAALHPPVTVP-DPAPPPPPAPA 57

Query: 237 PPSGPPRPGMPNAPPPRPGMPPPPGAPVFRPGMPPPPPNAQQQQQNQQQ 285
             + P      +        P  PG     P +        +   +   
Sbjct: 58  AGNPPDTVTGDSVLQRILRGPTGPGTTSLAPAVRYGRQPGPEAPASAPP 106

>3v1v_A 2-MIB synthase, 2-methylisoborneol synthase; class I terpenoid cyclase fold, DDXXXXD motif, NDXXSXXXE MOT methylisoborneol biosynthesis; HET: GST; 1.80A {Streptomyces coelicolor} PDB: 3v1x_A* Length = 433

 Score = 42.1 bits (98), Expect = 1e-04
 Identities = 23/140 (16%), Positives = 29/140 (20%), Gaps = 13/140 (9%)

Query: 143 GMMQPQISRPPIPQLSAPPMTYPATSGGPPVIRPPGQ-MPPPVYPGQGPPMARGPPPQGP 201
           G                  M  P+ S             PP   P   PP    P    P
Sbjct: 2   GSSHHHHHHSSGLVPRGSHMVIPSASVTSAASDFLAALHPPVTVPDPAPPPPPAPAAGNP 61

Query: 202 PQGFGVRPPQQFPMPPQQFGQRPMVPPPPGPMMRGPPSGPPRPGMPNAPPPRPGMPPPPG 261
           P                    + ++  P GP              P  P      PP  G
Sbjct: 62  P-----------DTVTGDSVLQRILRGPTGPGTTSLAPAVRYGRQP-GPEAPASAPPAAG 109

Query: 262 APVFRPGMPPPPPNAQQQQQ 281
             V      P P     + +
Sbjct: 110 RAVPGLYHHPVPEPDPVRVE 129

>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 1752

 Score = 45.8 bits (108), Expect = 1e-05
 Identities = 33/178 (18%), Positives = 43/178 (24%), Gaps = 24/178 (13%)

Query: 125  QAQPGLAGPVRGVGGPAPGMMQPQISRPPIPQLSAP--------PMTYPATSGGPPVIRP 176
             A P LAG   G      G   P    P +              P+    + G       
Sbjct: 1463 TAVPTLAGSGMGTSQLPEGAGTPYERSPMVDSGFVGSPDAAAFSPLVQGGSEGREGFGDY 1522

Query: 177  PGQMPPPVYPGQGPPMARGPPPQGPPQGFGVRPPQQFPMPPQQFGQRPMVPPPPG----- 231
                    Y G   P    P       G+G+  P   P  P        +P  P      
Sbjct: 1523 GLLGAASPYKGVQSPGYTSPFSSAMSPGYGLTSPSYSPSSPGYSTSPAYMPSSPSYSPTS 1582

Query: 232  ------PMMRGPPSGPPRPGMPNAPPPRPGMPP-----PPGAPVFRPGMPPPPPNAQQ 278
                       P S    P  P+     P   P      P +P + P  P   P +  
Sbjct: 1583 PSYSPTSPSYSPTSPSYSPTSPSYSATSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPS 1640

>3dzy_A Retinoic acid receptor RXR-alpha; DNA-binding, HOST-virus interaction, metal-binding, nucleus, receptor, transcription, transcription regulation, zinc-FIN activator; HET: DNA REA BRL; 3.10A {Homo sapiens} PDB: 3dzu_A* 3e00_A* Length = 467

 Score = 44.3 bits (104), Expect = 3e-05
 Identities = 23/118 (19%), Positives = 32/118 (27%), Gaps = 5/118 (4%)

Query: 146 QPQISRPPIPQLSAPPMTYPATSGGPPVIRPPGQMPPPVYPGQGPPMARGPPPQGPPQGF 205
              ++ P      A P  +P+     P I  PGQ+  P+     P    GPP        
Sbjct: 21  NSSLTSPTGRGSMAAPSLHPSLG---PGIGSPGQLHSPISTLSSPINGMGPPFSVISSPM 77

Query: 206 GVRPPQQFPMPPQQFGQRPMVPPPPGPMMRGPPSGPPRPGMPNAPPPRPGMPPPPGAP 263
           G  P           G     P    PM     S   +P +      +    P     
Sbjct: 78  G--PHSMSVPTTPTLGFSTGSPQLSSPMNPVSSSEDIKPPLGLNGVLKVPAHPSGNMA 133

>3dzy_A Retinoic acid receptor RXR-alpha; DNA-binding, HOST-virus interaction, metal-binding, nucleus, receptor, transcription, transcription regulation, zinc-FIN activator; HET: DNA REA BRL; 3.10A {Homo sapiens} PDB: 3dzu_A* 3e00_A* Length = 467

 Score = 42.0 bits (98), Expect = 2e-04
 Identities = 27/135 (20%), Positives = 35/135 (25%), Gaps = 6/135 (4%)

Query: 152 PPIPQLSAPPMTYPATSGGPPVIRPPGQMPPPVYPGQGPPMARGPPPQGPPQGFGVRPPQ 211
             +        T   +S   P  R     P   +P  GP +  G P Q       +  P 
Sbjct: 7   HHVDDDDKMFSTQVNSSLTSPTGRGSMAAPSL-HPSLGPGI--GSPGQLHSPISTLSSPI 63

Query: 212 QFPMPPQQFGQRPMVP---PPPGPMMRGPPSGPPRPGMPNAPPPRPGMPPPPGAPVFRPG 268
               PP      PM P     P     G  +G P+   P  P        PP        
Sbjct: 64  NGMGPPFSVISSPMGPHSMSVPTTPTLGFSTGSPQLSSPMNPVSSSEDIKPPLGLNGVLK 123

Query: 269 MPPPPPNAQQQQQNQ 283
           +P  P          
Sbjct: 124 VPAHPSGNMASFTKH 138

>2z73_A Rhodopsin; visual pigment, GQ-type, G-protein coupled receptor, chromophore, glycoprotein, lipoprotein, membrane, palmitate phosphorylation; HET: BOG RET PLM TWT PC1; 2.50A {Todarodes pacificus} PDB: 3aym_A* 3ayn_A* 2ziy_A* Length = 448

 Score = 43.4 bits (102), Expect = 5e-05
 Identities = 24/84 (28%), Positives = 29/84 (34%), Gaps = 4/84 (4%)

Query: 165 PATSGGPPVIRPPGQMPPPVYPGQGPPMARGPPPQGPPQGFGVRPPQQFPMPPQQFGQRP 224
           P+                       PP    PPPQG P      PPQ    PPQ +  + 
Sbjct: 364 PSADAAQMKEMMAMMQKMQQQQAAYPPQGYAPPPQGYPPQ--GYPPQ--GYPPQGYPPQG 419

Query: 225 MVPPPPGPMMRGPPSGPPRPGMPN 248
             PPP G   +G P   P  G+ N
Sbjct: 420 YPPPPQGAPPQGAPPAAPPQGVDN 443

>2z73_A Rhodopsin; visual pigment, GQ-type, G-protein coupled receptor, chromophore, glycoprotein, lipoprotein, membrane, palmitate phosphorylation; HET: BOG RET PLM TWT PC1; 2.50A {Todarodes pacificus} PDB: 3aym_A* 3ayn_A* 2ziy_A* Length = 448

 Score = 40.7 bits (95), Expect = 4e-04
 Identities = 32/89 (35%), Positives = 37/89 (41%), Gaps = 20/89 (22%)

Query: 156 QLSAPPMTYPATSGGPPVIRPPGQMPPPVYPGQGPPMARGPPPQG-PPQGFGVRPPQQFP 214
           Q+                  P G  PPP    QG P  +G PPQG PPQG    PPQ +P
Sbjct: 370 QMKEMMAMMQKMQQQQAAYPPQGYAPPP----QGYP-PQGYPPQGYPPQG---YPPQGYP 421

Query: 215 MPPQQFGQRPMVPPPPGPMMRGPPSGPPR 243
            PPQ         PP G     PP+ PP+
Sbjct: 422 PPPQGA-------PPQG----APPAAPPQ 439

>2z73_A Rhodopsin; visual pigment, GQ-type, G-protein coupled receptor, chromophore, glycoprotein, lipoprotein, membrane, palmitate phosphorylation; HET: BOG RET PLM TWT PC1; 2.50A {Todarodes pacificus} PDB: 3aym_A* 3ayn_A* 2ziy_A* Length = 448

 Score = 40.3 bits (94), Expect = 5e-04
 Identities = 31/97 (31%), Positives = 34/97 (35%), Gaps = 11/97 (11%)

Query: 188 QGPPMARGPPPQGPPQGFGVRPPQQFPMPPQQFGQRPMVPPPPGPMMRGPPSGPPRPGMP 247
              P A     +           QQ   PPQ +   P   PP G     PP G P    P
Sbjct: 361 DAAPSADAAQMKEMMAMMQKMQQQQAAYPPQGYAPPPQGYPPQGY----PPQGYP----P 412

Query: 248 NAPPPRPGMPPPPGAPVFRPGMPP-PPPNAQQQQQNQ 283
              PP+   PPP GAP    G PP  PP     Q  Q
Sbjct: 413 QGYPPQGYPPPPQGAPPQ--GAPPAAPPQGVDNQAYQ 447

>1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ... Length = 1733

 Score = 43.5 bits (102), Expect = 6e-05
 Identities = 29/184 (15%), Positives = 40/184 (21%), Gaps = 13/184 (7%)

Query: 113  AAGRGVPAAPLVQAQPGLAGPVRGVGGPAPGMMQPQISRPPIPQLSAPPMTYPATSGGPP 172
            +   G+  A L      +  P+   G                   +  P      +   P
Sbjct: 1474 SNESGLVNADLDVKDELMFSPLVDSGSNDAMAGGFTAYGGADYGEATSPFGAYGEAPTSP 1533

Query: 173  VIRPPGQMPPPVYPGQGPPMARGPPPQGPPQGFGVRPPQQFPMPPQQFGQRPMVPP---- 228
                      P  P   P     P        +    P   P  P      P   P    
Sbjct: 1534 GFGVSSPGFSPTSPTYSPTS---PAYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPS 1590

Query: 229  -PPGPMMRGPPSGPPRPGMPNAPPPRPGMPP-----PPGAPVFRPGMPPPPPNAQQQQQN 282
              P      P S    P  P+  P  P   P      P +P + P  P   P +      
Sbjct: 1591 YSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPT 1650

Query: 283  QQQQ 286
                
Sbjct: 1651 SPSY 1654

>1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ... Length = 1733

 Score = 42.0 bits (98), Expect = 2e-04
 Identities = 25/147 (17%), Positives = 39/147 (26%), Gaps = 5/147 (3%)

Query: 144  MMQPQISRPPIPQLSAPPMTYPATSGGPPVIRPPGQMPPPVYPGQGP---PMARGPPPQG 200
            M+  +     +P+     +      G  P     G +   +         P+        
Sbjct: 1444 MIDEESLVKYMPEQKITEIEDGQDGGVTPYSNESGLVNADLDVKDELMFSPLVDSGSNDA 1503

Query: 201  PPQGFGVRPPQQFPMPPQQFGQRPMVPPPPGPMMRGPPSGPPRPGM-PNAPPPRPGMPPP 259
               GF       +      FG     P  PG  +  P   P  P   P +P   P  P  
Sbjct: 1504 MAGGFTAYGGADYGEATSPFGAYGEAPTSPGFGVSSPGFSPTSPTYSPTSPAYSPTSPSY 1563

Query: 260  -PGAPVFRPGMPPPPPNAQQQQQNQQQ 285
             P +P + P  P   P +         
Sbjct: 1564 SPTSPSYSPTSPSYSPTSPSYSPTSPS 1590

>1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ... Length = 1733

 Score = 41.6 bits (97), Expect = 2e-04
 Identities = 38/196 (19%), Positives = 49/196 (25%), Gaps = 25/196 (12%)

Query: 88   GPPPPEESRAKAVSASAVAGPGIGRAAGRGVPAAPLVQAQPGLAGPVRGVGGPAPGMMQP 147
            G    E +        A   PG G ++    P +P          P      P      P
Sbjct: 1513 GADYGEATSPFGAYGEAPTSPGFGVSSPGFSPTSPTYSPTSPAYSPTSPSYSPTSPSYSP 1572

Query: 148  QISRPPIPQLSAPPMTYPATSGGPPVIRPPGQMPPPVYPGQGPPMARGPPPQGPPQGFGV 207
                           T P+ S   P   P      P  P   P  +    P  P   +  
Sbjct: 1573 ---------------TSPSYSPTSPSYSPTSPSYSPTSPSYSP-TSPSYSPTSP--SYSP 1614

Query: 208  RPPQQFPMPPQQFGQRPMVPPPPGPMMRGPPSGPPRPGMPNAPPPRPGMPPP-----PGA 262
              P   P  P      P   P         PS  P    P+  P  P   P      P +
Sbjct: 1615 TSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTS--PSYSPTSPAYSPTSPSYSPTS 1672

Query: 263  PVFRPGMPPPPPNAQQ 278
            P + P  P   P +  
Sbjct: 1673 PSYSPTSPSYSPTSPS 1688

>3tx7_B Nuclear receptor subfamily 5 group A member 2; LRH-1, beta-catenin, armadillo repeat, nuclear receptor LIGA binding domain, protein binding; HET: P6L; 2.76A {Homo sapiens} Length = 352

 Score = 40.4 bits (94), Expect = 4e-04
 Identities = 24/139 (17%), Positives = 34/139 (24%), Gaps = 4/139 (2%)

Query: 151 RPPIPQLSAPPMTYPATSGGPPVIRPPGQMPPPVYPGQGPPMARGPPPQGPPQGFGVRPP 210
              + Q+     +    S     I    +  P       PP      P          PP
Sbjct: 4   LEAMSQVIQAMPSDLTISSAIQNIHSASKGLPL-NHAALPPTDYDRSPFVTSPISMTMPP 62

Query: 211 QQFPMPPQQFGQRPMVPPP---PGPMMRGPPSGPPRPGMPNAPPPRPGMPPPPGAPVFRP 267
                  Q +G  P        P P    P S      M +     P   P     + + 
Sbjct: 63  HGSLQGYQTYGHFPSRAIKSEYPDPYTSSPESIMGYSYMDSYQTSSPASIPHLILELLKC 122

Query: 268 GMPPPPPNAQQQQQNQQQQ 286
               P   A+     QQ+Q
Sbjct: 123 EPDEPQVQAKIMAYLQQEQ 141

>3lvg_A Clathrin heavy chain 1; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} PDB: 3lvh_A Length = 624

 Score = 40.7 bits (95), Expect = 4e-04
 Identities = 11/47 (23%), Positives = 14/47 (29%), Gaps = 4/47 (8%)

Query: 214 PMPPQQFGQRPMVPPPPGPMMRGPPSGPPRPGMPN--APPPRPGMPP 258
             P      + M     GP +  PP  P   G        P+PG   
Sbjct: 578 TQPIVYGQPQLM--LTAGPSVAVPPQAPFGYGYTAPAYGQPQPGFGY 622

>3lvg_A Clathrin heavy chain 1; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} PDB: 3lvh_A Length = 624

 Score = 39.6 bits (92), Expect = 8e-04
 Identities = 13/46 (28%), Positives = 17/46 (36%), Gaps = 4/46 (8%)

Query: 176 PPGQMPPPVYPGQGPPMARGPPPQGPPQGFGVRPPQQFPMPPQQFG 221
           P     P +    GP +    PPQ  P G+G      +  P   FG
Sbjct: 580 PIVYGQPQLMLTAGPSV--AVPPQ-APFGYGY-TAPAYGQPQPGFG 621

>4emh_A Probable U6 snRNA-associated SM-like protein LSM4; SM fold, mRNA decay, PRE-mRNA splicing, LSM proteins, RNA BI protein; 2.20A {Schizosaccharomyces pombe} Length = 105

 Score = 37.8 bits (88), Expect = 4e-04
 Identities = 12/69 (17%), Positives = 22/69 (31%), Gaps = 13/69 (18%)

Query: 13 INYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLG 72
              + V +++G    G     D +MNL L +                T  + +    L 
Sbjct: 25 QGRPILVELKNGETFNGHLENCDNYMNLTLREVIR-------------TMPDGDKFFRLP 71

Query: 73 LVLLRGEEV 81
             +RG  +
Sbjct: 72 ECYIRGNNI 80

>2z6g_A B-catenin; FULL-length, beta-catenin, cell adhesion; 3.40A {Danio rerio} Length = 780

 Score = 40.0 bits (93), Expect = 6e-04
 Identities = 16/102 (15%), Positives = 24/102 (23%), Gaps = 2/102 (1%)

Query: 159 APPMTYPATSGGPPVIRPPGQMPPPVYPGQGPPMARGPPPQGPPQGFGVRPPQQFPMPPQ 218
           +  +T       P      G +   +     P   R   P       G        M P 
Sbjct: 674 SVELTSSLFRTEPMTWNETGDLGLDIGAQGEPLGYRQDDPSYRSFHSGGYGQDAMGMDPM 733

Query: 219 QFGQRPM-VPPPPGPMMRGPPSGPPRPGMPNAPPPRPGMPPP 259
              +     P P  P+   P  G     + +  PP       
Sbjct: 734 MEHEMAGHHPGPDYPVDGLPDLGHT-QDLIDGLPPGDSNQLA 774

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	286
3pgw_B	231	SM B; protein-RNA complex, U1 snRNA, SM fold, SM c	100.0
1d3b_B	91	Protein (small nuclear ribonucleoprotein associat	99.94
3s6n_G	76	Small nuclear ribonucleoprotein G; SMN complex, SM	99.88
1h64_1	75	SnRNP SM-like protein; SM fold, spliceosome, snRNP	99.86
4emg_A	93	Probable U6 snRNA-associated SM-like protein LSM3;	99.86
1i4k_A	77	Putative snRNP SM-like protein; core snRNP domain,	99.86
1th7_A	81	SnRNP-2, small nuclear riboprotein protein; archae	99.86
3bw1_A	96	SMX4 protein, U6 snRNA-associated SM-like protein	99.86
4emk_C	113	U6 snRNA-associated SM-like protein LSM7; SM fold,	99.86
4emk_B	75	U6 snRNA-associated SM-like protein LSM6; SM fold,	99.85
4emk_A	94	U6 snRNA-associated SM-like protein LSM5; SM fold,	99.85
2fwk_A	121	U6 snRNA-associated SM-like protein LSM5; structur	99.84
1i8f_A	81	Putative snRNP SM-like protein; beta barrel-like S	99.84
1ljo_A	77	Archaeal SM-like protein AF-SM2; snRNP, core snRNP	99.84
1mgq_A	83	SM-like protein; LSM, RNA-binding, archea, RNA bin	99.84
1b34_A	119	Protein (small nuclear ribonucleoprotein SM D1); s	99.82
1b34_B	118	Protein (small nuclear ribonucleoprotein SM D2); s	99.82
3s6n_F	86	Small nuclear ribonucleoprotein F; SMN complex, SM	99.82
3s6n_E	92	Small nuclear ribonucleoprotein E; SMN complex, SM	99.81
1d3b_A	75	Protein (small nuclear ribonucleoprotein SM D3); s	99.8
1n9r_A	93	SMF, small nuclear ribonucleoprotein F, snRNP-F, S	99.8
4emh_A	105	Probable U6 snRNA-associated SM-like protein LSM4;	99.77
2y9a_D	126	Small nuclear ribonucleoprotein SM D3; splicing-RN	99.76
1m5q_A	130	SMAP3, small nuclear ribonucleoprotein homolog, SM	99.72
1y96_A	86	Gemin6, SIP2, GEM-associated protein 6; SM fold, p	98.77
2vxe_A	88	CG10686-PA; EDC3, CAR-1, P-bodies, decapping, mRNA	97.42
2fb7_A	95	SM-like protein, LSM-14_N (RAP55); DR.13312, BC055	97.27
4a53_A	125	EDC3; RNA binding protein; NMR {Schizosaccharomyce	96.38
1y96_B	85	Gemin7, SIP3, GEM-associated protein 7; SM fold, p	96.11
2vc8_A	84	Enhancer of mRNA-decapping protein 3; P-BODY compo	94.8
2qtx_A	71	Uncharacterized protein MJ1435; HFQ, SM, RNA-bindi	94.5
1ycy_A	71	Conserved hypothetical protein; structural genomic	94.02
1kq1_A	77	HFQ, HOST factor for Q beta; hexamer, RNA binding	94.01
2ylb_A	74	Protein HFQ; RNA-binding protein, LSM protein, RNA	93.94
3ahu_A	78	Protein HFQ; SM-like motif, protein-RNA complex, t	93.77
3sb2_A	79	Protein HFQ; SM-like, RNA chaperone, chaperone; 2.	92.99
2y90_A	104	Protein HFQ; RNA-binding protein, SM-like, RNA cha	92.96
1u1s_A	82	HFQ protein; SM-like bacterial protein, riken stru	92.5
3rux_A	270	BIRA bifunctional protein; biotin-protein ligase,	90.42
1ib8_A	164	Conserved protein SP14.3; nucleic acid binding pro	90.37
2rm4_A	103	CG6311-PB, DM EDC3; enhancer of mRNA decapping, P-	88.37
3hfn_A	72	ASL2047 protein; HFQ, SM, RNA-binding protein, sRN	87.66
3pgw_B	231	SM B; protein-RNA complex, U1 snRNA, SM fold, SM c	87.09
3hfo_A	70	SSR3341 protein; HFQ, SM, RNA-binding protein, sRN	84.34
2xk0_A	69	Polycomb protein PCL; transcription, aromatic CAGE	84.01
1bia_A	321	BIRA bifunctional protein; transcription regulatio	83.9

>3pgw_B SM B; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_A

Probab=100.00  E-value=4.1e-49  Score=357.10  Aligned_cols=189  Identities=57%  Similarity=0.998  Sum_probs=167.4

Q ss_pred             CCchhhhHHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCce
Q 023166            1 MSMSKSSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEE   80 (286)
Q Consensus         1 m~~~k~skL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGen   80 (286)
                      |+|+|+++|++||||+|+|+|+|||+|+|+|++||+||||||+||+||++++.|+++    +.+.+++|+||+|||||||
T Consensus         1 ~~v~k~~kL~klIdKrV~V~LkdGRel~GtLkgFDq~MNLVL~Da~E~~~ik~k~~k----~~~~~~~R~LGlV~IRGdn   76 (231)
T 3pgw_B            1 MTVGKSSKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSK----QAEREEKRVLGLVLLRGEN   76 (231)
T ss_pred             CCcCchHHHHHhcCCeEEEEECCCcEEEEEEEEEcccccEEecCEEEEEeccCcccc----cccccceeEeceEEECCCc
Confidence            899999999999999999999999999999999999999999999999976554332    2356789999999999999


Q ss_pred             eEEeeecCCCCChhhhhhhccccCCCCCCccccCCCCCCC-CCCcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 023166           81 VISMTVEGPPPPEESRAKAVSASAVAGPGIGRAAGRGVPA-APLVQAQPGLAGPVRGVGGPAPGMMQPQISRPPIPQLSA  159 (286)
Q Consensus        81 IVSIsVe~PPp~d~~~~~~~~~~~~~Gpg~~r~aGRG~p~-~~~~~~~~gL~gp~~gvggp~~~~m~p~~~~~~~~~~~a  159 (286)
                      |++|++|+++++|+++.+++++++++|||++|+||||+++ .++++++.||+||++|||+|++++|+||++    ..+.+
T Consensus        77 IV~Isve~pPp~d~~~~~~~~~~~~~gpg~~~~agrg~~~~~~~~~~~~gl~gp~~g~g~p~~~~~~p~~~----~~~~~  152 (231)
T 3pgw_B           77 LVSMTVEGPPPKDTGIARVPLAGAAGGPGIGRAAGRGIPAGVPMPQAPAGLAGPVRGVGGPSQQVMTPQGR----GTVAA  152 (231)
T ss_pred             EEEEEecCCCCCCcccccccccccCCCCcccccccCCCCccCCCCCCccccccccccccCCCcccccCCCc----ccccc
Confidence            9999999999999999888888899999999999999997 567889999999999999999999999985    46666


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 023166          160 PPMTYPATSGGPPVIRPPGQMPPPVYPGQGPPMARGPPPQGPPQ  203 (286)
Q Consensus       160 ~~~~~~~~~~~~p~~~ppg~~~~~~~~~~~p~~~~g~ppp~~~~  203 (286)
                      ......++.-+++..++++....+      ++++++++|++.|.
T Consensus       153 ~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~g~~~  190 (231)
T 3pgw_B          153 AAAAATASIAGAPTQYPPGRGGPP------PPMGRGAPPPGMMG  190 (231)
T ss_pred             cccccccccccCCcccCccccCCC------CccccCCCCCcccC
Confidence            666666666677888888877543      78999999999887

>1d3b_B Protein (small nuclear ribonucleoprotein associat B); snRNP, splicing, core snRNP domain, systemic lupus eryth SLE, RNA binding protein; HET: CIT; 2.00A {Homo sapiens} SCOP: b.38.1.1 PDB: 2y9a_A 2y9b_A 2y9c_A 2y9d_A

Probab=99.94  E-value=2.2e-27  Score=185.17  Aligned_cols=90  Identities=63%  Similarity=1.116  Sum_probs=72.0

Q ss_pred             CCchhhhHHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCce
Q 023166            1 MSMSKSSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEE   80 (286)
Q Consensus         1 m~~~k~skL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGen   80 (286)
                      |+++++++|.+|+|++|+|+|+|||+|+|+|+|||+||||||+||+|++++..++.+    ..+.+++|.||++||||+|
T Consensus         1 m~~~~~~~L~~~~~k~V~V~l~~gr~~~G~L~~~D~~mNlvL~d~~E~~~~~~~~~~----~~~~~~~~~lg~v~iRG~~   76 (91)
T 1d3b_B            1 MTVGKSSKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSK----QAEREEKRVLGLVLLRGEN   76 (91)
T ss_dssp             ------CCCGGGTTSEEEEEETTCCEEEEEEEECCTTCCEEEEEEEEEEEECCSSTT----SCCEEEEEEEEEEEECGGG
T ss_pred             CCCChhHHHHHHcCCcEEEEECCCeEEEEEEEEECCCCeEEecCEEEEeeccccccc----cccCccEeECCEEEECCCe
Confidence            889999999999999999999999999999999999999999999999865443221    1235678999999999999


Q ss_pred             eEEeeecCCCCChh
Q 023166           81 VISMTVEGPPPPEE   94 (286)
Q Consensus        81 IVSIsVe~PPp~d~   94 (286)
                      |++|+++++++.|+
T Consensus        77 I~~i~~~~~~~~~~   90 (91)
T 1d3b_B           77 LVSMTVEGPPPKDT   90 (91)
T ss_dssp             EEEEEEEECCC---
T ss_pred             EEEEEcCCCCCCCC
Confidence            99999999998764

>3s6n_G Small nuclear ribonucleoprotein G; SMN complex, SMN-gemin2 complex, U-rich snRNA, SM fold, SM C SNRNPS, snRNP biogenesis, PRE-mRNA splicing; 2.50A {Homo sapiens} PDB: 2y9b_G 2y9c_G 2y9d_G 3cw1_G 3pgw_G* 2y9a_G

Probab=99.88  E-value=3.8e-23  Score=157.15  Aligned_cols=74  Identities=26%  Similarity=0.601  Sum_probs=52.3

Q ss_pred             CCchhhhHHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCce
Q 023166            1 MSMSKSSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEE   80 (286)
Q Consensus         1 m~~~k~skL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGen   80 (286)
                      ||..+.++|.+|+|++|+|+|+|||+|+|+|++||+||||+|+||+|+++.              .+++.||+++|||+|
T Consensus         1 ms~~~~~~L~~~~~k~V~V~Lk~gr~~~G~L~~~D~~mNlvL~~~~e~~~~--------------~~~~~lg~v~iRG~~   66 (76)
T 3s6n_G            1 MSKAHPPELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATS--------------GQQNNIGMVVIRGNS   66 (76)
T ss_dssp             -------------CCEEEEEETTTEEEEEEEEEECTTCCEEEEEEEECCCC------------------CBSSEEECSSS
T ss_pred             CCCcchHHHHHhCCCeEEEEECCCcEEEEEEEEECCcceEEEeceEEEccC--------------CcEeEcCEEEECCCe
Confidence            788888999999999999999999999999999999999999999998641              246899999999999


Q ss_pred             eEEeeecC
Q 023166           81 VISMTVEG   88 (286)
Q Consensus        81 IVSIsVe~   88 (286)
                      |++|+..+
T Consensus        67 I~~i~~~d   74 (76)
T 3s6n_G           67 IIMLEALE   74 (76)
T ss_dssp             EEEEEC--
T ss_pred             EEEEEecc
Confidence            99998543

>1h64_1 SnRNP SM-like protein; SM fold, spliceosome, snRNP core; 1.9A {Pyrococcus abyssi} SCOP: b.38.1.1 PDB: 1m8v_A*

Probab=99.86  E-value=5.3e-22  Score=149.71  Aligned_cols=73  Identities=22%  Similarity=0.475  Sum_probs=64.8

Q ss_pred             CCchhhhHHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCce
Q 023166            1 MSMSKSSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEE   80 (286)
Q Consensus         1 m~~~k~skL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGen   80 (286)
                      |+..-.+.|.+|+|++|+|+|+|||+|+|+|++||+||||+|+||+|++.              .++++.||+++|||+|
T Consensus         1 m~~~P~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~d~~e~~~--------------~~~~~~lg~v~iRG~~   66 (75)
T 1h64_1            1 MAERPLDVIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQD--------------GEVVKRYGKIVIRGDN   66 (75)
T ss_dssp             --CCHHHHHHTTTTSEEEEEETTSEEEEEEEEEECTTCCEEEEEEEEEET--------------TEEEEEEEEEEECGGG
T ss_pred             CCchHHHHHHHHCCCEEEEEECCCCEEEEEEEEEeCCCCeEEeeEEEEee--------------CCceeECCEEEECCCE
Confidence            56666778999999999999999999999999999999999999999974              1468899999999999


Q ss_pred             eEEeeec
Q 023166           81 VISMTVE   87 (286)
Q Consensus        81 IVSIsVe   87 (286)
                      |++|+..
T Consensus        67 I~~i~~~   73 (75)
T 1h64_1           67 VLAISPT   73 (75)
T ss_dssp             EEEEEEC
T ss_pred             EEEEEeC
Confidence            9999764

>4emg_A Probable U6 snRNA-associated SM-like protein LSM3; SM fold, mRNA decay, LSM proteins, RNA binding protein; 2.70A {Schizosaccharomyces pombe}

Probab=99.86  E-value=4.4e-22  Score=157.32  Aligned_cols=83  Identities=23%  Similarity=0.492  Sum_probs=61.7

Q ss_pred             chhhhHHHHh-cCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCcee
Q 023166            3 MSKSSKMLQF-INYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEV   81 (286)
Q Consensus         3 ~~k~skL~ql-IgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenI   81 (286)
                      +....+|+++ +|++|+|+|+|||+|+|+|++||+||||||+||+|+++.+.++++.. +..+++++|.||++||||+||
T Consensus         7 ~~~Pl~lL~~~~~~~V~V~l~~gr~~~G~L~~~D~~mNlvL~d~~E~~~~~~~~~~~~-~~~~~~~~r~lG~v~iRG~nV   85 (93)
T 4emg_A            7 VAEPLDLVRLSLDEIVYVKLRGDRELNGRLHAYDEHLNMVLGDAEEIVTIFDDEETDK-DKALKTIRKHYEMLFVRGDSV   85 (93)
T ss_dssp             --CTTHHHHTTTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEEEC---------------CEEEEEEEEEECGGGE
T ss_pred             cCCCHHHHHHhCCCEEEEEECCCcEEEEEEEEECCcccEEeecEEEEEeccccCCccc-cccccccEeEeceEEECCCeE
Confidence            3455677665 99999999999999999999999999999999999997644322100 002346789999999999999


Q ss_pred             EEeee
Q 023166           82 ISMTV   86 (286)
Q Consensus        82 VSIsV   86 (286)
                      ++|+.
T Consensus        86 v~I~p   90 (93)
T 4emg_A           86 ILIAP   90 (93)
T ss_dssp             EEEEC
T ss_pred             EEEEe
Confidence            99974

>1i4k_A Putative snRNP SM-like protein; core snRNP domain, RNA binding protein; HET: CIT; 2.50A {Archaeoglobus fulgidus} SCOP: b.38.1.1 PDB: 1i5l_A*

Probab=99.86  E-value=8e-22  Score=149.19  Aligned_cols=74  Identities=30%  Similarity=0.460  Sum_probs=65.1

Q ss_pred             CCchhhhHHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCce
Q 023166            1 MSMSKSSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEE   80 (286)
Q Consensus         1 m~~~k~skL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGen   80 (286)
                      |+..-.+.|.+|+|++|+|+|+|||+|+|+|++||+||||+|+||+|++.              .++++.||+++|||+|
T Consensus         1 m~~~P~~~L~~~~~~~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~--------------~~~~~~lg~v~iRG~~   66 (77)
T 1i4k_A            1 MPPRPLDVLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQN--------------GEVVRKVGSVVIRGDT   66 (77)
T ss_dssp             --CCHHHHHHTTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEEET--------------TEEEEEEEEEEECGGG
T ss_pred             CCccHHHHHHHhCCCEEEEEEcCCCEEEEEEEEEcCCCCeEEeeEEEEec--------------CCcEeECCEEEECCCE
Confidence            55566678999999999999999999999999999999999999999974              1467899999999999


Q ss_pred             eEEeeecC
Q 023166           81 VISMTVEG   88 (286)
Q Consensus        81 IVSIsVe~   88 (286)
                      |++|+..+
T Consensus        67 I~~i~~~d   74 (77)
T 1i4k_A           67 VVFVSPAP   74 (77)
T ss_dssp             EEEEEECC
T ss_pred             EEEEEeCC
Confidence            99998643

>1th7_A SnRNP-2, small nuclear riboprotein protein; archaea, SM protein, SM fold, SS-SM1, RNA binding protein; 1.68A {Sulfolobus solfataricus} SCOP: b.38.1.1

Probab=99.86  E-value=8.3e-22  Score=151.00  Aligned_cols=73  Identities=26%  Similarity=0.499  Sum_probs=64.4

Q ss_pred             CchhhhHHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCcee
Q 023166            2 SMSKSSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEV   81 (286)
Q Consensus         2 ~~~k~skL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenI   81 (286)
                      +..-.+.|.+|+|++|+|+|+|||+|+|+|++||+||||||+||+|++.              .++++.||+++|||+||
T Consensus         7 ~~~P~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~d~~e~~~--------------~~~~~~lg~v~iRG~~I   72 (81)
T 1th7_A            7 AETAHKVLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQS--------------DGSGKKLGTIVIRGDNV   72 (81)
T ss_dssp             CHHHHHHHHHHTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEECS--------------SSCEEEEEEEEECGGGE
T ss_pred             ccchHHHHHHhCCCeEEEEEcCCcEEEEEEEEEcCCCCEEEccEEEEec--------------CCceeECCEEEECCCEE
Confidence            3445578999999999999999999999999999999999999999874              13578999999999999


Q ss_pred             EEeeecC
Q 023166           82 ISMTVEG   88 (286)
Q Consensus        82 VSIsVe~   88 (286)
                      ++|+..+
T Consensus        73 ~~i~~~~   79 (81)
T 1th7_A           73 ILISPLQ   79 (81)
T ss_dssp             EEEEEC-
T ss_pred             EEEEecC
Confidence            9998654

>3bw1_A SMX4 protein, U6 snRNA-associated SM-like protein LSM3; RNA-binding protein, SM protein, ring, HOMO octamer, mRNA processing; 2.50A {Saccharomyces cerevisiae}

Probab=99.86  E-value=9.8e-22  Score=155.79  Aligned_cols=76  Identities=28%  Similarity=0.411  Sum_probs=65.3

Q ss_pred             hhHHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEee
Q 023166            6 SSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMT   85 (286)
Q Consensus         6 ~skL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIs   85 (286)
                      ...|.+|+|++|+|+|+|||+|+|+|+|||+||||||+||+|++....+.       ...+.+|.||++||||+||++|+
T Consensus        12 ~~~L~~~i~k~V~V~Lk~gr~~~G~L~~fD~~mNlVL~d~~E~~~~~~~~-------~~~~~~r~lG~v~IRG~nVv~I~   84 (96)
T 3bw1_A           12 LDLLKLNLDERVYIKLRGARTLVGTLQAFDSHCNIVLSDAVETIYQLNNE-------ELSESERRCEMVFIRGDTVTLIS   84 (96)
T ss_dssp             HHHHGGGTTSEEEEEEGGGCEEEEEEEEECTTCCEEEEEEEEEEECCSTT-------CCCEEEEEEEEEEECGGGEEEEE
T ss_pred             HHHHHHHCCCeEEEEECCCcEEEEEEEEECCCCcEEEcCEEEEecccccc-------ccCcceeEcCEEEECCCEEEEEE
Confidence            45788999999999999999999999999999999999999998743221       12457899999999999999997


Q ss_pred             ecC
Q 023166           86 VEG   88 (286)
Q Consensus        86 Ve~   88 (286)
                      ...
T Consensus        85 ~~d   87 (96)
T 3bw1_A           85 TPS   87 (96)
T ss_dssp             CCC
T ss_pred             ecC
Confidence            543

>4emk_C U6 snRNA-associated SM-like protein LSM7; SM fold, mRNA decay and PRE-mRNA splicing, LSM proteins, RNA protein; 2.30A {Schizosaccharomyces pombe} PDB: 3swn_C

Probab=99.86  E-value=8e-22  Score=161.22  Aligned_cols=75  Identities=32%  Similarity=0.529  Sum_probs=57.2

Q ss_pred             hHHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEeee
Q 023166            7 SKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMTV   86 (286)
Q Consensus         7 skL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIsV   86 (286)
                      .+|.+|||++|+|+|+|||+|+|+|+|||+||||||+||+|++....  +     ....+++|.||+|||||+||++|+.
T Consensus        26 ~~L~~~l~k~V~V~L~dGr~~~G~L~~fD~~mNLVL~d~~E~~~~~~--~-----~~~~~~~r~lG~v~IRG~nIv~I~~   98 (113)
T 4emk_C           26 LDLSRYQDQRIQATFTGGRQITGILKGFDQLMNLVLDDVEEQLRNPE--D-----GKLTGAIRKLGLVVVRGTTLVLIAP   98 (113)
T ss_dssp             ------CCSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEEC----------------CCEEEEEEEEECTTTEEEEEE
T ss_pred             HHHHHHcCCcEEEEEeCCeEEEEEEEEEcCcccEEEeeEEEEEcCCC--C-----cccccceeEccEEEECCCeEEEEEe
Confidence            57889999999999999999999999999999999999999986311  0     0224678999999999999999986


Q ss_pred             cC
Q 023166           87 EG   88 (286)
Q Consensus        87 e~   88 (286)
                      .+
T Consensus        99 ~d  100 (113)
T 4emk_C           99 MD  100 (113)
T ss_dssp             CC
T ss_pred             cC
Confidence            54

>4emk_B U6 snRNA-associated SM-like protein LSM6; SM fold, mRNA decay and PRE-mRNA splicing, LSM proteins, RNA protein; 2.30A {Schizosaccharomyces pombe} PDB: 3swn_B

Probab=99.85  E-value=1.4e-21  Score=147.91  Aligned_cols=73  Identities=22%  Similarity=0.365  Sum_probs=65.6

Q ss_pred             CCchhhhHHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCce
Q 023166            1 MSMSKSSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEE   80 (286)
Q Consensus         1 m~~~k~skL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGen   80 (286)
                      |+..-.+.|.+|+|++|+|+|+|||+|+|+|++||+||||+|+||+|++.              .++++.||+++|||+|
T Consensus         1 m~~~P~~~L~~~~~k~V~V~Lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~--------------~~~~~~lg~v~iRG~~   66 (75)
T 4emk_B            1 MDSSPNEFLNKVIGKKVLIRLSSGVDYKGILSCLDGYMNLALERTEEYVN--------------GKKTNVYGDAFIRGNN   66 (75)
T ss_dssp             CCSHHHHHHHHTTTSEEEEECTTSCEEEEEEEEECTTCEEEEEEEEEEET--------------TEEEEEEEEEEEEGGG
T ss_pred             CCCchHHHHHHhCCCeEEEEEcCCcEEEEEEEEEcCcceEEEccEEEEec--------------CCcccEecEEEEcCCe
Confidence            66667788999999999999999999999999999999999999999863              1357899999999999


Q ss_pred             eEEeeec
Q 023166           81 VISMTVE   87 (286)
Q Consensus        81 IVSIsVe   87 (286)
                      |++|+..
T Consensus        67 I~~i~~~   73 (75)
T 4emk_B           67 VLYVSAL   73 (75)
T ss_dssp             SSEEEEC
T ss_pred             EEEEEec
Confidence            9999753

>4emk_A U6 snRNA-associated SM-like protein LSM5; SM fold, mRNA decay and PRE-mRNA splicing, LSM proteins, RNA protein; 2.30A {Schizosaccharomyces pombe} PDB: 3swn_A

Probab=99.85  E-value=3.1e-21  Score=153.43  Aligned_cols=71  Identities=23%  Similarity=0.391  Sum_probs=62.5

Q ss_pred             hHHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEeee
Q 023166            7 SKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMTV   86 (286)
Q Consensus         7 skL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIsV   86 (286)
                      .-|.+|+|++|+|+|+|||+|+|+|++||+||||||+||+|++. +            .++++.||+++|||+||++|+.
T Consensus        23 ~lL~~~l~k~V~V~Lk~gr~~~G~L~gfD~~mNlvL~d~~E~~~-~------------~~~~~~lg~v~IRG~nI~~i~p   89 (94)
T 4emk_A           23 ELIDKCIGSNLWVIMKSEREFAGTLVGFDDYVNIVLKDVTEYDT-V------------TGVTEKHSEMLLNGNGMCMLIP   89 (94)
T ss_dssp             HHHHHTTTSEEEEEESSSEEEEEEEEEECTTCCEEEEEEEEEET-T------------TCCEEEEEEEEECSTTEEEEEE
T ss_pred             HHHHHHcCCeEEEEECCCcEEEEEEEEEcccCCeEeeeEEEEec-C------------CCcEeEcCEEEEcCCEEEEEEe
Confidence            45779999999999999999999999999999999999999973 1            2358899999999999999998


Q ss_pred             cCCC
Q 023166           87 EGPP   90 (286)
Q Consensus        87 e~PP   90 (286)
                      .+.|
T Consensus        90 ~~~p   93 (94)
T 4emk_A           90 GGKP   93 (94)
T ss_dssp             CC--
T ss_pred             CCCC
Confidence            8754

>2fwk_A U6 snRNA-associated SM-like protein LSM5; structural genomics, structural genomics consortium, SGC, DNA binding protein; 2.14A {Cryptosporidium parvum} SCOP: b.38.1.1 PDB: 3pgg_A

Probab=99.84  E-value=1.1e-21  Score=161.32  Aligned_cols=85  Identities=22%  Similarity=0.363  Sum_probs=64.1

Q ss_pred             hHHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCC-cccccceeEeceEEecCceeEEee
Q 023166            7 SKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNT-NEEREDRRTLGLVLLRGEEVISMT   85 (286)
Q Consensus         7 skL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~-~~e~eekR~LGlVLIRGenIVSIs   85 (286)
                      ..|.+|+|++|+|+|+|||+|+|+|++||+||||||+||+|+++...++.+.... ....+++|.||++||||+||++|+
T Consensus        31 ~lL~~~l~k~V~V~Lk~Gr~~~G~L~~fD~~mNlVL~d~~E~~~~~~~~~~~~~g~~~~~~~~r~lG~v~IRG~nVv~I~  110 (121)
T 2fwk_A           31 ALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGGNKKLKRVMVNRLETILLSGNNVAMLV  110 (121)
T ss_dssp             HHHHHTBTSBCEEEETTTEEECCEEEEECTTCCEEEESCCEEEC---------------CEECCCCSEEEECGGGEEEEE
T ss_pred             HHHHHHcCCeEEEEECCCcEEEEEEEEEcccCCeEeceEEEEEeccccccccccCcccccccceEcceEEECCCEEEEEE
Confidence            4567999999999999999999999999999999999999998642111000000 001223899999999999999999


Q ss_pred             ecCCCC
Q 023166           86 VEGPPP   91 (286)
Q Consensus        86 Ve~PPp   91 (286)
                      ..+.++
T Consensus       111 ~~~~~~  116 (121)
T 2fwk_A          111 PGGDPD  116 (121)
T ss_dssp             SSSCC-
T ss_pred             ecCCCC
Confidence            888765

>1i8f_A Putative snRNP SM-like protein; beta barrel-like SMAP monomers form 35-stranded beta-sheet I heptamer, structural genomics; 1.75A {Pyrobaculum aerophilum} SCOP: b.38.1.1 PDB: 1lnx_A*

Probab=99.84  E-value=5.4e-21  Score=146.66  Aligned_cols=67  Identities=27%  Similarity=0.479  Sum_probs=61.0

Q ss_pred             hhHHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEee
Q 023166            6 SSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMT   85 (286)
Q Consensus         6 ~skL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIs   85 (286)
                      .+.|.+|++++|+|+|+|||+|+|+|++||+||||||+||+|+ .              .++++.||+++|||+||++|+
T Consensus        13 ~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~d~~e~-~--------------~~~~~~lg~v~iRG~~I~~i~   77 (81)
T 1i8f_A           13 GATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEI-I--------------DGNVYKRGTMVVRGENVLFIS   77 (81)
T ss_dssp             HHHHHTTTTSEEEEEEGGGEEEEEEEEEECTTCCEEEEEEEEE-E--------------TTEEEEEEEEEECGGGEEEEE
T ss_pred             HHHHHHHCCCeEEEEEcCCcEEEEEEEEEcCCCeeEEccEEEE-c--------------CCcccCCCEEEECCCEEEEEE
Confidence            4578899999999999999999999999999999999999998 2              135789999999999999998


Q ss_pred             ec
Q 023166           86 VE   87 (286)
Q Consensus        86 Ve   87 (286)
                      ..
T Consensus        78 ~~   79 (81)
T 1i8f_A           78 PV   79 (81)
T ss_dssp             EC
T ss_pred             eC
Confidence            64

>1ljo_A Archaeal SM-like protein AF-SM2; snRNP, core snRNP domain, RNA binding protein, unknown F; 1.95A {Archaeoglobus fulgidus} SCOP: b.38.1.1

Probab=99.84  E-value=6.9e-21  Score=144.43  Aligned_cols=70  Identities=30%  Similarity=0.470  Sum_probs=63.2

Q ss_pred             hhhhHHHHhcCCEEEEEEeCC-cEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeE
Q 023166            4 SKSSKMLQFINYRMRVTIQDG-RQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVI   82 (286)
Q Consensus         4 ~k~skL~qlIgkRVRVtLqDG-R~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIV   82 (286)
                      .-.+.|.+|++++|+|+|+|| |+|+|+|++||+||||+|+||+|+++              .++++.||+++|||+||+
T Consensus         5 ~P~~~L~~~~~~~v~V~lk~g~~~~~G~L~~~D~~mNlvL~d~~e~~~--------------~~~~~~lg~v~iRG~nI~   70 (77)
T 1ljo_A            5 LPNQMVKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECKG--------------EEKVRSLGEIVLRGNNVV   70 (77)
T ss_dssp             CHHHHHHHTTTSEEEEEETTCSSEEEEEEEEECTTCCEEEEEEEEEET--------------TEEEEEEEEEEECGGGEE
T ss_pred             chHHHHHHHCCCEEEEEEeCCCEEEEEEEEEECCcceEEEeeEEEEec--------------CCcEeECCeEEEeCCeEE
Confidence            445688999999999999999 99999999999999999999999874              135789999999999999


Q ss_pred             Eeeec
Q 023166           83 SMTVE   87 (286)
Q Consensus        83 SIsVe   87 (286)
                      +|+..
T Consensus        71 ~i~~~   75 (77)
T 1ljo_A           71 LIQPQ   75 (77)
T ss_dssp             EEEEC
T ss_pred             EEEeC
Confidence            99864

>1mgq_A SM-like protein; LSM, RNA-binding, archea, RNA binding protein; 1.70A {Methanothermobacterthermautotrophicus} SCOP: b.38.1.1 PDB: 1i81_A 1loj_A* 1jbm_A 1jri_A

Probab=99.84  E-value=6.9e-21  Score=146.84  Aligned_cols=66  Identities=33%  Similarity=0.583  Sum_probs=60.7

Q ss_pred             hhHHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEee
Q 023166            6 SSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMT   85 (286)
Q Consensus         6 ~skL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIs   85 (286)
                      ...|.+|+|++|+|+|+|||+|+|+|++||+||||+|+||+|++.              .++++.||+++|||+||++|+
T Consensus        17 ~~~L~~~~~~~V~V~Lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~--------------~~~~~~lg~v~IRG~~I~~i~   82 (83)
T 1mgq_A           17 LDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELED--------------GEVTRRLGTVLIRGDNIVYIS   82 (83)
T ss_dssp             THHHHHTTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEEET--------------TEEEEEEEEEEECGGGEEEEE
T ss_pred             HHHHHHhCCCEEEEEEcCCcEEEEEEEEECCCceeEEccEEEEec--------------CCcccCCCEEEECCCEEEEEE
Confidence            357889999999999999999999999999999999999999974              146889999999999999986

>1b34_A Protein (small nuclear ribonucleoprotein SM D1); snRNP, splicing, spliceosome, core snRNP domain, systemi erythematosus, SLE, RNA binding protein; 2.50A {Homo sapiens} SCOP: b.38.1.1 PDB: 2y9a_B 2y9b_B 2y9c_B 2y9d_B 3cw1_B 3pgw_X* 3s6n_A

Probab=99.82  E-value=1.7e-20  Score=154.05  Aligned_cols=71  Identities=17%  Similarity=0.294  Sum_probs=62.8

Q ss_pred             hHHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEeee
Q 023166            7 SKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMTV   86 (286)
Q Consensus         7 skL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIsV   86 (286)
                      ..|.+++|++|.|+|+||++|+|+|++||+||||||+||+|+..              ..+++.|+++||||+||++|++
T Consensus         5 ~~L~~~~gk~V~V~Lk~g~~~~G~L~~~D~~MNlvL~d~~e~~~--------------~~~~~~lg~v~IRG~nI~~I~~   70 (119)
T 1b34_A            5 RFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLK--------------NREPVQLETLSIRGNNIRYFIL   70 (119)
T ss_dssp             HHHHTCTTCEEEEEETTCCEEEEEEEEECTTCCEEEEEEEEECT--------------TSCCEEEEEEEECGGGEEEEEC
T ss_pred             HHHHHhCCCEEEEEEcCCCEEEEEEEEEcccceEEeccEEEecC--------------CCceeEcceEEEcCCeEEEEEe
Confidence            56889999999999999999999999999999999999999853              1245899999999999999998


Q ss_pred             cCCCC
Q 023166           87 EGPPP   91 (286)
Q Consensus        87 e~PPp   91 (286)
                      .+.-.
T Consensus        71 pd~l~   75 (119)
T 1b34_A           71 PDSLP   75 (119)
T ss_dssp             CTTCC
T ss_pred             ccccc
Confidence            76533

>1b34_B Protein (small nuclear ribonucleoprotein SM D2); snRNP, splicing, spliceosome, core snRNP domain, systemi erythematosus, SLE, RNA binding protein; 2.50A {Homo sapiens} SCOP: b.38.1.1 PDB: 2y9a_C 2y9b_C 2y9c_C 2y9d_C 3cw1_C 3pgw_Y* 3s6n_B

Probab=99.82  E-value=1.8e-20  Score=153.47  Aligned_cols=83  Identities=28%  Similarity=0.475  Sum_probs=58.7

Q ss_pred             hhHHHHhc--CCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEE
Q 023166            6 SSKMLQFI--NYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVIS   83 (286)
Q Consensus         6 ~skL~qlI--gkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVS   83 (286)
                      .+.|.+++  |++|+|+|+|||+|+|+|++||+||||||+||+|++....+.++........+.+|.||++||||+||++
T Consensus        29 l~lL~~~~~~~k~V~V~Lk~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~nVv~  108 (118)
T 1b34_B           29 LSVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKGKKKSKPVNKDRYISKMFLRGDSVIV  108 (118)
T ss_dssp             HHHHHHHHHHTCEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEC-------------------CEEEEEEEECGGGEEE
T ss_pred             HHHHHHHhcCCcEEEEEECCCcEEEEEEEEeCCceEEEEeCEEEEEecccccccccccccccccccCcCeEEEcCCEEEE
Confidence            34577888  5999999999999999999999999999999999986543321110000123457899999999999999


Q ss_pred             eeecC
Q 023166           84 MTVEG   88 (286)
Q Consensus        84 IsVe~   88 (286)
                      |+...
T Consensus       109 I~~~~  113 (118)
T 1b34_B          109 VLRNP  113 (118)
T ss_dssp             EEECC
T ss_pred             EEeCc
Confidence            98653

>3s6n_F Small nuclear ribonucleoprotein F; SMN complex, SMN-gemin2 complex, U-rich snRNA, SM fold, SM C SNRNPS, snRNP biogenesis, PRE-mRNA splicing; 2.50A {Homo sapiens} PDB: 2y9b_F 2y9c_F 2y9d_F 3cw1_F 3pgw_F* 2y9a_F

Probab=99.82  E-value=3.5e-20  Score=144.36  Aligned_cols=69  Identities=22%  Similarity=0.270  Sum_probs=61.8

Q ss_pred             hhHHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEee
Q 023166            6 SSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMT   85 (286)
Q Consensus         6 ~skL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIs   85 (286)
                      ...|.+|+|++|+|+|+|||+|+|+|++||+||||+|+||+|++.              .++++.||+++|||+||++|+
T Consensus         8 ~~~L~~~~~k~V~V~Lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~--------------g~~~~~lg~v~IRG~nI~~i~   73 (86)
T 3s6n_F            8 KPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYID--------------GALSGHLGEVLIRCNNVLYIR   73 (86)
T ss_dssp             HHHHHHHTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEEET--------------TEEEEEESSEEECGGGEEEEE
T ss_pred             HHHHHHhCCCeEEEEEcCCeEEEEEEEEEcCceEEEEeeEEEEcC--------------CceeeEccEEEEeCCeEEEEE
Confidence            456889999999999999999999999999999999999999863              135789999999999999998


Q ss_pred             ecC
Q 023166           86 VEG   88 (286)
Q Consensus        86 Ve~   88 (286)
                      ..+
T Consensus        74 ~~d   76 (86)
T 3s6n_F           74 GVE   76 (86)
T ss_dssp             ECC
T ss_pred             eCC
Confidence            754

>3s6n_E Small nuclear ribonucleoprotein E; SMN complex, SMN-gemin2 complex, U-rich snRNA, SM fold, SM C SNRNPS, snRNP biogenesis, PRE-mRNA splicing; 2.50A {Homo sapiens} PDB: 2y9b_E 2y9c_E 2y9d_E 3cw1_E 3pgw_E* 2y9a_E

Probab=99.81  E-value=2.8e-20  Score=147.23  Aligned_cols=69  Identities=28%  Similarity=0.556  Sum_probs=61.2

Q ss_pred             hhHHHHhcCCEEEEEE----eCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCcee
Q 023166            6 SSKMLQFINYRMRVTI----QDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEV   81 (286)
Q Consensus         6 ~skL~qlIgkRVRVtL----qDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenI   81 (286)
                      .+-|.+|++++|+|+|    +|||+|+|+|++||+||||||+||+|++..             .++++.||++||||+||
T Consensus        18 l~lL~~~l~~~v~V~l~~~~~~gr~~~G~L~gfD~~mNlvL~d~~E~~~~-------------~~~~~~lg~v~iRG~nV   84 (92)
T 3s6n_E           18 INLIFRYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEIHSK-------------TKSRKQLGRIMLKGDNI   84 (92)
T ss_dssp             HHHHHHHHHHTCEEEEEESSSCSSEEEEEEEEECTTCCEEEEEEEEECSS-------------SCCEEEEEEEEECGGGE
T ss_pred             HHHHHHHhCCCEEEEEEEEecCCEEEEEEEEEEcCcCcEEEeeeEEEecC-------------CCceeEcCeEEEeCCEE
Confidence            3557799999999999    999999999999999999999999999741             24688999999999999


Q ss_pred             EEeeec
Q 023166           82 ISMTVE   87 (286)
Q Consensus        82 VSIsVe   87 (286)
                      ++|+..
T Consensus        85 ~~i~~~   90 (92)
T 3s6n_E           85 TLLQSV   90 (92)
T ss_dssp             EEEEEC
T ss_pred             EEEEeC
Confidence            999753

>1d3b_A Protein (small nuclear ribonucleoprotein SM D3); snRNP, splicing, core snRNP domain, systemic lupus eryth SLE, RNA binding protein; HET: CIT; 2.00A {Homo sapiens} SCOP: b.38.1.1

Probab=99.80  E-value=1.8e-19  Score=136.88  Aligned_cols=73  Identities=16%  Similarity=0.204  Sum_probs=61.7

Q ss_pred             CCchhhhH-HHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCc
Q 023166            1 MSMSKSSK-MLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGE   79 (286)
Q Consensus         1 m~~~k~sk-L~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGe   79 (286)
                      |+++...+ |.+++|++|+|+|+||++|+|+|.+||.||||+|+||+|+.+              ..+++.+|.++|||+
T Consensus         1 ~~~~~P~~~L~~~~g~~V~VeLk~g~~~~G~L~~~D~~MNl~L~~~~e~~~--------------~~~~~~lg~v~IRG~   66 (75)
T 1d3b_A            1 MSIGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYR--------------DGRVAQLEQVYIRGC   66 (75)
T ss_dssp             ---CCHHHHHHHTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEECT--------------TSCEEEEEEEEECGG
T ss_pred             CCccCHHHHHHHhCCCEEEEEECCCcEEEEEEEEEccceeEEEEeEEEECC--------------CCcEEEcCeEEEeCC
Confidence            56655555 568999999999999999999999999999999999999863              124789999999999


Q ss_pred             eeEEeeec
Q 023166           80 EVISMTVE   87 (286)
Q Consensus        80 nIVSIsVe   87 (286)
                      ||++|++.
T Consensus        67 nI~~i~lP   74 (75)
T 1d3b_A           67 KIRFLILP   74 (75)
T ss_dssp             GEEEEEEC
T ss_pred             EEEEEEcC
Confidence            99999875

>1n9r_A SMF, small nuclear ribonucleoprotein F, snRNP-F, SM protein F; heptamer, translation; 2.80A {Saccharomyces cerevisiae} SCOP: b.38.1.1 PDB: 1n9s_A

Probab=99.80  E-value=7.8e-20  Score=144.68  Aligned_cols=68  Identities=24%  Similarity=0.360  Sum_probs=59.6

Q ss_pred             hhHHHHhcCCEEEEEEeCC-cEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEe
Q 023166            6 SSKMLQFINYRMRVTIQDG-RQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISM   84 (286)
Q Consensus         6 ~skL~qlIgkRVRVtLqDG-R~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSI   84 (286)
                      ...|.+++|++|+|+|+|| |+|+|+|++||+||||+|+||+|++.              .++++.||++||||+||++|
T Consensus        23 ~~~L~~~i~k~V~V~Lk~g~~~~~G~L~~~D~~MNlvL~d~~E~~~--------------~~~~~~lg~v~IRG~nI~~I   88 (93)
T 1n9r_A           23 KPFLKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVA--------------GVSHGTLGEIFIRCNNVLYI   88 (93)
T ss_dssp             ---CGGGTTSEEEEEESSTTEEEEEEEEECCTTTCEEEEEEEEEET--------------TEEEEECCSEEECGGGEEEE
T ss_pred             HHHHHHhCCCEEEEEEcCCCEEEEEEEEEEccccEEEEeeEEEEcC--------------CCeEeEcCEEEEcCCeEEEE
Confidence            3568899999999999999 99999999999999999999999863              13578999999999999999


Q ss_pred             eec
Q 023166           85 TVE   87 (286)
Q Consensus        85 sVe   87 (286)
                      +..
T Consensus        89 ~~~   91 (93)
T 1n9r_A           89 REL   91 (93)
T ss_dssp             EEC
T ss_pred             EeC
Confidence            764

>4emh_A Probable U6 snRNA-associated SM-like protein LSM4; SM fold, mRNA decay, PRE-mRNA splicing, LSM proteins, RNA BI protein; 2.20A {Schizosaccharomyces pombe}

Probab=99.77  E-value=5.5e-19  Score=142.96  Aligned_cols=68  Identities=16%  Similarity=0.238  Sum_probs=55.0

Q ss_pred             HHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEeeec
Q 023166            8 KMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMTVE   87 (286)
Q Consensus         8 kL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIsVe   87 (286)
                      .|.+++|++|+|+|+|||+|+|+|++||.||||+|+||+|+..             +.++++.||++||||+||++|++.
T Consensus        20 lL~~~igk~V~V~Lk~G~~~~G~L~~~D~~MNlvL~d~~e~~~-------------dg~~~~~lg~v~IRG~nI~~I~~p   86 (105)
T 4emh_A           20 LLNATQGRPILVELKNGETFNGHLENCDNYMNLTLREVIRTMP-------------DGDKFFRLPECYIRGNNIKYLRIQ   86 (105)
T ss_dssp             ------CCEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEECT-------------TSCEEEEEEEEEECGGGEEEEEC-
T ss_pred             HHHHhCCCEEEEEECCCCEEEEEEEEEcCCceEEEEEEEEEcc-------------CCceeeEcCeEEEeCCeEEEEecC
Confidence            4678999999999999999999999999999999999999853             123578999999999999999876


Q ss_pred             C
Q 023166           88 G   88 (286)
Q Consensus        88 ~   88 (286)
                      +
T Consensus        87 d   87 (105)
T 4emh_A           87 D   87 (105)
T ss_dssp             -
T ss_pred             H
Confidence            5

>2y9a_D Small nuclear ribonucleoprotein SM D3; splicing-RNA complex, PRE-mRNA splicing, spliceosome, snRNP biogenesis, SM site, SM fold, heteromeric heptameric ring; 3.60A {Homo sapiens} PDB: 2y9b_D 2y9c_D 2y9d_D 3pgw_Z* 3cw1_D

Probab=99.76  E-value=1.5e-18  Score=144.47  Aligned_cols=76  Identities=14%  Similarity=0.152  Sum_probs=62.9

Q ss_pred             CCchhhh-HHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCc
Q 023166            1 MSMSKSS-KMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGE   79 (286)
Q Consensus         1 m~~~k~s-kL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGe   79 (286)
                      |++.... .|.++++++|.|+|+||++|+|+|.+||.||||+|+||+|+...              .+++.|++|||||+
T Consensus         1 ~~~~~P~~~L~~~~gk~V~VeLknG~~~~G~L~~~D~~MNi~L~dv~e~~~~--------------g~~~~l~~v~IRGn   66 (126)
T 2y9a_D            1 MSIGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRD--------------GRVAQLEQVYIRGS   66 (126)
T ss_dssp             ---CCSHHHHHSCSSCEEEEEESSCCEEEEEEEEECTTSCEEEEEEEEECTT--------------SCCEEEEEEEECGG
T ss_pred             CCcccHHHHHHHhCCCEEEEEECCCcEEEEEEEEEcCceEEEEeeEEEEcCC--------------CcEeecccEEEeCC
Confidence            5554444 46689999999999999999999999999999999999998530              13679999999999


Q ss_pred             eeEEeeecCCC
Q 023166           80 EVISMTVEGPP   90 (286)
Q Consensus        80 nIVSIsVe~PP   90 (286)
                      ||++|++.+--
T Consensus        67 nI~~I~lpd~l   77 (126)
T 2y9a_D           67 KIRFLILPDML   77 (126)
T ss_dssp             GEEEEECCSSC
T ss_pred             EEEEEEccccc
Confidence            99999987743

>1m5q_A SMAP3, small nuclear ribonucleoprotein homolog, SM-like P; OB-like fold, B-sheet toroid, 14-MER, cadmium-binding site, translation; 2.00A {Pyrobaculum aerophilum} SCOP: b.38.1.1

Probab=99.72  E-value=1.2e-17  Score=139.79  Aligned_cols=70  Identities=13%  Similarity=0.269  Sum_probs=62.9

Q ss_pred             hHHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEeee
Q 023166            7 SKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMTV   86 (286)
Q Consensus         7 skL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIsV   86 (286)
                      +.|.+++|++|+|+|+|||+|+|+|++||+||||+|+||+|+.                  ++.||+++|||+||++|+.
T Consensus         3 ~~L~~~igk~V~V~Lk~G~~~~G~L~~~D~~MNlvL~d~~E~~------------------~~~lg~v~IRG~nI~~I~~   64 (130)
T 1m5q_A            3 AELNNLLGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASNKA------------------GEKFNRVFIMYRYIVHIDS   64 (130)
T ss_dssp             HHHHHTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEECTT------------------CCEEEEEEECGGGEEEEEE
T ss_pred             hHHHHhCCCeEEEEECCCcEEEEEEEEEcccceeEEeeEEEEc------------------CCEeceEEEeCCeEEEEEc
Confidence            5789999999999999999999999999999999999999862                  2578999999999999999


Q ss_pred             cCCCCChhh
Q 023166           87 EGPPPPEES   95 (286)
Q Consensus        87 e~PPp~d~~   95 (286)
                      .+.. .|..
T Consensus        65 ~d~~-~d~~   72 (130)
T 1m5q_A           65 TERR-IDMR   72 (130)
T ss_dssp             CCCC-CCHH
T ss_pred             CCcc-cCHH
Confidence            8876 5553

>1y96_A Gemin6, SIP2, GEM-associated protein 6; SM fold, protein complex, RNA binding protein; 2.00A {Homo sapiens}

Probab=98.77  E-value=1.6e-08  Score=79.57  Aligned_cols=66  Identities=18%  Similarity=0.231  Sum_probs=56.6

Q ss_pred             hhHHHHhcCCEEEEEEeCCcEEEEEEEEec-cccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEe
Q 023166            6 SSKMLQFINYRMRVTIQDGRQLVGKFMAFD-RHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISM   84 (286)
Q Consensus         6 ~skL~qlIgkRVRVtLqDGR~fvGtLlAFD-KhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSI   84 (286)
                      ..+|.+||||+|+|+|.||++|+|+|.+|| ...||||.|+.|                    +.....++|-|..|+.|
T Consensus         9 p~el~~li~KeV~V~l~dg~~y~G~l~tvDp~s~sIvL~n~~~--------------------~~~~~~~iI~G~aI~eI   68 (86)
T 1y96_A            9 PLEWQDYIYKEVRVTASEKNEYKGWVLTTDPVSANIVLVNFLE--------------------DGSMSVTGIMGHAVQTV   68 (86)
T ss_dssp             HHHHHHTTTCEEEEEETTTEEEEEEEEEECTTTCCEEEEEECT--------------------TSCEEEEEECGGGEEEE
T ss_pred             HHHHHhhcCCEEEEEEcCCCEEEEEEEEECCCceEEEEeeccc--------------------CCeEEEEEEecceEEEE
Confidence            457999999999999999999999999999 899999999821                    11236899999999999


Q ss_pred             eecCCCC
Q 023166           85 TVEGPPP   91 (286)
Q Consensus        85 sVe~PPp   91 (286)
                      .+.+.+.
T Consensus        69 ~v~~~~~   75 (86)
T 1y96_A           69 ETMNEGD   75 (86)
T ss_dssp             EEEECCC
T ss_pred             EEecchh
Confidence            9887654

>2vxe_A CG10686-PA; EDC3, CAR-1, P-bodies, decapping, mRNA decay, LSM proteins, translational repression, transcription; NMR {Drosophila melanogaster}

Probab=97.42  E-value=0.00072  Score=53.40  Aligned_cols=77  Identities=12%  Similarity=0.228  Sum_probs=60.8

Q ss_pred             HHhcCCEEEEEEeCCcEEEEEEEEecc-ccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEeeecC
Q 023166           10 LQFINYRMRVTIQDGRQLVGKFMAFDR-HMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMTVEG   88 (286)
Q Consensus        10 ~qlIgkRVRVtLqDGR~fvGtLlAFDK-hMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIsVe~   88 (286)
                      ..||+++|.++.+.+-.|+|+|..+|. ..-|.|.|+.-|-+..++..     .+.--....+..|+.||+.|..|+|.+
T Consensus         9 ~~yIGs~iSLISk~dIRYeGiL~~In~~~sTi~L~nVrsfGTEgR~~~-----~~ipp~~~vy~yIvFrgsDIKdL~V~~   83 (88)
T 2vxe_A            9 LPELGSKISLISKADIRYEGRLYTVDPQECTIALSSVRSFGTEDRDTQ-----FQIAPQSQIYDYILFRGSDIKDIRVVN   83 (88)
T ss_dssp             SCCTTCEEEEEETTTEEEEEEEEEEETTTTEEEEEEEEECCCTTTCCS-----SCCCCCCSCEEEEEEETTTEEEEEECC
T ss_pred             CcccCCeEEEEECCCceEEEEEeeecCcccEEEEEeeeEecCcCCCCC-----cccCCCCceeeEEEEccCCccEEEEec
Confidence            579999999999999999999999995 46799999998877543321     112223456689999999999999987


Q ss_pred             CCC
Q 023166           89 PPP   91 (286)
Q Consensus        89 PPp   91 (286)
                      .-+
T Consensus        84 ~~p   86 (88)
T 2vxe_A           84 NHT   86 (88)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            654

>2fb7_A SM-like protein, LSM-14_N (RAP55); DR.13312, BC055387, AAH55387, stronGly BENT five-stranded antiparallel beta- sheet, structural genomics, PSI; NMR {Danio rerio} SCOP: b.38.1.5 PDB: 2vxf_A

Probab=97.27  E-value=0.00064  Score=54.36  Aligned_cols=81  Identities=16%  Similarity=0.306  Sum_probs=59.6

Q ss_pred             hhHHHHhcCCEEEEEEeCCcEEEEEEEEec-cccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEe
Q 023166            6 SSKMLQFINYRMRVTIQDGRQLVGKFMAFD-RHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISM   84 (286)
Q Consensus         6 ~skL~qlIgkRVRVtLqDGR~fvGtLlAFD-KhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSI   84 (286)
                      +....+||+++|.++.+.+-.|+|+|..+| +..-|.|.|+.-|-+..++...     ..--....+..|+.||+.|..|
T Consensus        11 ~~~~~~~IGs~ISLISk~dIRYeGiL~~In~~~sTiaL~nVRsfGTEgR~~~~-----~ipp~~~vyeyIvFrGsDIKDL   85 (95)
T 2fb7_A           11 PSGGTPYIGSKISLISKAEIRYEGILYTIDTENSTVALAKVRSFGTEDRPTDR-----PIAPRDETFEYIIFRGSDIKDL   85 (95)
T ss_dssp             -----CCSSEEEEEEETTTEEEEEEEEEEETTTTEEEEESCCCCSCCSSSCSS-----CCCSCCCCSSCEEECSTTEEEE
T ss_pred             CCccCcccCCeEEEEECCCceEEEEEecccCccCEEEEEeeeEecccCCCCCC-----ccCCCCcceeEEEEcCCCcceE
Confidence            345678999999999999999999999999 4567899999888765332211     1122344668899999999999


Q ss_pred             eecCCCC
Q 023166           85 TVEGPPP   91 (286)
Q Consensus        85 sVe~PPp   91 (286)
                      +|.++|.
T Consensus        86 ~V~e~p~   92 (95)
T 2fb7_A           86 TVCEPPK   92 (95)
T ss_dssp             EESCCSC
T ss_pred             EEecCCC
Confidence            9987654

>4a53_A EDC3; RNA binding protein; NMR {Schizosaccharomyces pombe} PDB: 4a54_A

Probab=96.38  E-value=0.0029  Score=52.73  Aligned_cols=36  Identities=19%  Similarity=0.325  Sum_probs=32.1

Q ss_pred             HHHhcCCEEEEEEeCCcEEEEEEEEeccccceEe--Cce
Q 023166            9 MLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVL--GDC   45 (286)
Q Consensus         9 L~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVL--sD~   45 (286)
                      +.+||+|.|.|+|+||..+.|++..+|.. +|+|  +|+
T Consensus         7 ~sqFlGy~V~v~LkDgs~~qG~I~~vd~k-~LtL~~~~a   44 (125)
T 4a53_A            7 VADFYGSNVEVLLNNDSKARGVITNFDSS-NSILQLRLA   44 (125)
T ss_dssp             HHHHTTCEEEEEETTSCEEEEEEEEEETT-TTEEEEEET
T ss_pred             HHHhcCceEEEEECCCCEeeEEEEeecCC-eeEEecccc
Confidence            56999999999999999999999999955 6777  776

>1y96_B Gemin7, SIP3, GEM-associated protein 7; SM fold, protein complex, RNA binding protein; 2.00A {Homo sapiens}

Probab=96.11  E-value=0.014  Score=45.73  Aligned_cols=61  Identities=21%  Similarity=0.347  Sum_probs=46.7

Q ss_pred             HHHHhcCCEEEEEEeCCcEEEEEEEEeccc-cceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEeee
Q 023166            8 KMLQFINYRMRVTIQDGRQLVGKFMAFDRH-MNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMTV   86 (286)
Q Consensus         8 kL~qlIgkRVRVtLqDGR~fvGtLlAFDKh-MNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIsV   86 (286)
                      .|+...+++|.++|.++.++.|+|.|+|.. .|+..+|-+-                   ---.+...+||+..|++|++
T Consensus        23 ~l~~m~~~~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L~T-------------------PiGv~~eAlLR~~Dii~~sF   83 (85)
T 1y96_B           23 SLLAMVGHQVSFTLHEGVRVAAHFGATDLDVANFYVSQLQT-------------------PIGVQAEALLRCSDIISYTF   83 (85)
T ss_dssp             HHHHHTTSEEEEEEGGGCEEEEEEEEECTTCCEEEEEEECC-------------------TTCCEEEEEEEGGGEEEEEE
T ss_pred             HHHHhCCCceEEEEeCCeEEEEEEEecCcccceeEhhhcCC-------------------CcccchhhhhhcCCEEEEEe
Confidence            355678999999999999999999999954 4555443321                   12236688999999999997


Q ss_pred             c
Q 023166           87 E   87 (286)
Q Consensus        87 e   87 (286)
                      +
T Consensus        84 ~   84 (85)
T 1y96_B           84 K   84 (85)
T ss_dssp             C
T ss_pred             c
Confidence            6

>2vc8_A Enhancer of mRNA-decapping protein 3; P-BODY component, cytoplasm, SM-like protein, protein-binding; 1.31A {Homo sapiens}

Probab=94.80  E-value=0.055  Score=42.34  Aligned_cols=65  Identities=15%  Similarity=0.252  Sum_probs=51.6

Q ss_pred             HHhcCCEEEEEEeCCc-EEEEEEEEeccc-cceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEeeec
Q 023166           10 LQFINYRMRVTIQDGR-QLVGKFMAFDRH-MNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMTVE   87 (286)
Q Consensus        10 ~qlIgkRVRVtLqDGR-~fvGtLlAFDKh-MNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIsVe   87 (286)
                      .+||++.|.|...|.- .|.|.|..+|.+ -||.|.++  |+.     +          .+...-.|.+|+.-|..+.+.
T Consensus         5 ~~~iGs~VSi~c~d~lGvYQG~i~~vd~~~~tItL~~~--f~N-----G----------~~~~s~eVtls~~DI~~L~ii   67 (84)
T 2vc8_A            5 TDWLGSIVSINCGDSLGVYQGRVSAVDQVSQTISLTRP--FHN-----G----------VKCLVPEVTFRAGDITELKIL   67 (84)
T ss_dssp             CTTTTCEEEEECCTTTCEEEEEEEEEETTTTEEEEEEE--EET-----T----------EECSSSEEEEEGGGCSEEEEE
T ss_pred             ccccCCEEEEEECCCceEEEEEEEEeccCCCeEEEehh--hhC-----C----------CCCCCcEEEEEecChhheEEE
Confidence            4899999999999999 999999999977 47999999  432     1          122223499999999999887


Q ss_pred             CCCC
Q 023166           88 GPPP   91 (286)
Q Consensus        88 ~PPp   91 (286)
                      .-+.
T Consensus        68 ~~~~   71 (84)
T 2vc8_A           68 EIPG   71 (84)
T ss_dssp             ECCC
T ss_pred             ecCC
Confidence            6544

>2qtx_A Uncharacterized protein MJ1435; HFQ, SM, RNA-binding protein, sRNA, translational regulation, RNA binding protein; 2.50A {Methanocaldococcus jannaschii}

Probab=94.50  E-value=0.051  Score=41.26  Aligned_cols=31  Identities=10%  Similarity=0.172  Sum_probs=25.5

Q ss_pred             CCEEEEEEeCCcEEEEEEEEeccccceEeCc
Q 023166           14 NYRMRVTIQDGRQLVGKFMAFDRHMNLVLGD   44 (286)
Q Consensus        14 gkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD   44 (286)
                      +..|+|-|.||-.++|++++||+|+=|+-+|
T Consensus        25 ~~~Vtv~L~NG~~l~G~I~~fD~ftVll~~~   55 (71)
T 2qtx_A           25 GKKVKIFLRNGEVLDAEVTGVSNYEIMVKVG   55 (71)
T ss_dssp             TCEEEEEETTSCEEEEEEEEECSSEEEEEET
T ss_pred             CCcEEEEEeCCeEEEEEEEEEcceEEEEEeC
Confidence            4578888999999999999999998555333

>1ycy_A Conserved hypothetical protein; structural genomics, southeast collaboratory for structural genomics, secsg, protein structure initiative; 2.80A {Pyrococcus furiosus} SCOP: b.38.1.4

Probab=94.02  E-value=0.06  Score=40.52  Aligned_cols=42  Identities=14%  Similarity=0.362  Sum_probs=33.3

Q ss_pred             hHHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEee
Q 023166            7 SKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFR   49 (286)
Q Consensus         7 skL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r   49 (286)
                      ..|.+|.++||-|.+.....|+|+|.-||... |.|.|+..+.
T Consensus         9 ktL~~WKg~rvAv~vg~ehSFtGiledFDeEv-iLL~dV~D~~   50 (71)
T 1ycy_A            9 KVLKEWKGHKVAVSVGGDHSFTGTLEDFDEEV-ILLKDVVDVI   50 (71)
T ss_dssp             HHHHHHTTSEEEEEEC----CEEEEEEECSSE-EEEEEEEETT
T ss_pred             HHHHHhCCcEEEEEecCcceeeeehhhcCcce-eehhhHHHHh
Confidence            35788999999999999999999999999884 7889998765

>1kq1_A HFQ, HOST factor for Q beta; hexamer, RNA binding protein, translational regulator, SM motif; 1.55A {Staphylococcus aureus} SCOP: b.38.1.2 PDB: 1kq2_A

Probab=94.01  E-value=0.071  Score=40.88  Aligned_cols=34  Identities=18%  Similarity=0.261  Sum_probs=27.4

Q ss_pred             HHHhc--CCEEEEEEeCCcEEEEEEEEeccccceEe
Q 023166            9 MLQFI--NYRMRVTIQDGRQLVGKFMAFDRHMNLVL   42 (286)
Q Consensus         9 L~qlI--gkRVRVtLqDGR~fvGtLlAFDKhMNLVL   42 (286)
                      |+++.  ...|.|.|.+|-.++|++++||+|+=|+-
T Consensus        12 Ln~lrk~k~~VtI~L~nG~~l~G~I~~fD~f~VlL~   47 (77)
T 1kq1_A           12 LENFKANQTEVTVFFLNGFQMKGVIEEYDKYVVSLN   47 (77)
T ss_dssp             HHHHHHHTCEEEEEETTSCEEEEEEEEECSSEEEEE
T ss_pred             HHHHHhcCCeEEEEEeCCCEEEEEEEEECCcEEEEE
Confidence            34444  56888899999999999999999985553

>2ylb_A Protein HFQ; RNA-binding protein, LSM protein, RNA chaperone; 1.15A {Salmonella enterica subsp} PDB: 2yht_A 1hk9_A 2ylc_A* 3gib_A* 3rer_A* 3qo3_A* 3res_A*

Probab=93.94  E-value=0.072  Score=40.53  Aligned_cols=33  Identities=18%  Similarity=0.382  Sum_probs=26.9

Q ss_pred             HHHhc--CCEEEEEEeCCcEEEEEEEEeccccceE
Q 023166            9 MLQFI--NYRMRVTIQDGRQLVGKFMAFDRHMNLV   41 (286)
Q Consensus         9 L~qlI--gkRVRVtLqDGR~fvGtLlAFDKhMNLV   41 (286)
                      |+++.  ...|.|.|.+|-.++|++++||+|+=|+
T Consensus        14 L~~lrk~k~~Vti~L~nG~~l~G~I~~fD~f~vlL   48 (74)
T 2ylb_A           14 LNALRRERVPVSIYLVNGIKLQGQIESFDQFVILL   48 (74)
T ss_dssp             HHHHHHHTCCEEEEETTSCEEEEEEEEECSSEEEE
T ss_pred             HHHHHhcCCcEEEEEeCCCEEEEEEEEECCcEEEE
Confidence            44444  5688899999999999999999998444

>3ahu_A Protein HFQ; SM-like motif, protein-RNA complex, translation-RNA complex; 2.20A {Bacillus subtilis} PDB: 3hsb_A

Probab=93.77  E-value=0.08  Score=40.80  Aligned_cols=29  Identities=31%  Similarity=0.387  Sum_probs=25.3

Q ss_pred             CCEEEEEEeCCcEEEEEEEEeccccceEe
Q 023166           14 NYRMRVTIQDGRQLVGKFMAFDRHMNLVL   42 (286)
Q Consensus        14 gkRVRVtLqDGR~fvGtLlAFDKhMNLVL   42 (286)
                      ...|+|-|.||..++|++++||+|+=|+-
T Consensus        23 ~~~Vtv~L~nG~~l~G~I~~fD~f~VlL~   51 (78)
T 3ahu_A           23 NTYVTVFLLNGFQLRGQVKGFDNFTVLLE   51 (78)
T ss_dssp             TCCEEEEETTSCEEEEEEEEECSSEEEEE
T ss_pred             CCcEEEEEeCCeEEEEEEEEEcceEEEEE
Confidence            56888999999999999999999985553

>3sb2_A Protein HFQ; SM-like, RNA chaperone, chaperone; 2.63A {Herbaspirillum seropedicae} SCOP: b.38.1.2

Probab=92.99  E-value=0.07  Score=41.23  Aligned_cols=33  Identities=18%  Similarity=0.338  Sum_probs=25.9

Q ss_pred             HHHhcCC--EEEEEEeCCcEEEEEEEEeccccceE
Q 023166            9 MLQFINY--RMRVTIQDGRQLVGKFMAFDRHMNLV   41 (286)
Q Consensus         9 L~qlIgk--RVRVtLqDGR~fvGtLlAFDKhMNLV   41 (286)
                      |+++..+  .|.|.|.+|-.++|++++||+|+=|+
T Consensus        13 Ln~lrk~k~~VtI~LvnG~~L~G~I~~fD~f~VlL   47 (79)
T 3sb2_A           13 LNALRKEHVPVSIYLVNGIKLQGHVESFDQYVVLL   47 (79)
T ss_dssp             HHHHHHTTCCEEEEETTSCEEEEEEEEECSSEEEE
T ss_pred             HHHHHhcCCeEEEEEeCCCEEEEEEEEECCcEEEE
Confidence            4444444  58888999999999999999998444

>2y90_A Protein HFQ; RNA-binding protein, SM-like, RNA chaperone; 2.25A {Escherichia coli} PDB: 3qhs_A

Probab=92.96  E-value=0.089  Score=42.58  Aligned_cols=34  Identities=18%  Similarity=0.335  Sum_probs=26.6

Q ss_pred             HHHhcCC--EEEEEEeCCcEEEEEEEEeccccceEe
Q 023166            9 MLQFINY--RMRVTIQDGRQLVGKFMAFDRHMNLVL   42 (286)
Q Consensus         9 L~qlIgk--RVRVtLqDGR~fvGtLlAFDKhMNLVL   42 (286)
                      |+++..+  .|.|.|.+|-.++|++++||+|+=|+-
T Consensus        14 Ln~lrk~k~~VtI~LvNG~~L~G~I~~fD~f~VlL~   49 (104)
T 2y90_A           14 LNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLK   49 (104)
T ss_dssp             HHHHHHTTCCEEEEETTSCEEEEEEEEECSSEEEEE
T ss_pred             HHHHHhcCCcEEEEEeCCCEEEEEEEEECCcEEEEE
Confidence            4444444  788889999999999999999985443

>1u1s_A HFQ protein; SM-like bacterial protein, riken structural genomics/proteomics initiative, RSGI, structural genomics, RNA binding protein; 1.60A {Pseudomonas aeruginosa} SCOP: b.38.1.2 PDB: 1u1t_A 3qui_A* 3m4g_A 3inz_A

Probab=92.50  E-value=0.14  Score=39.77  Aligned_cols=28  Identities=21%  Similarity=0.459  Sum_probs=24.6

Q ss_pred             CCEEEEEEeCCcEEEEEEEEeccccceE
Q 023166           14 NYRMRVTIQDGRQLVGKFMAFDRHMNLV   41 (286)
Q Consensus        14 gkRVRVtLqDGR~fvGtLlAFDKhMNLV   41 (286)
                      ...|+|-|.||-.++|++++||+|+=|+
T Consensus        19 ~~~Vtv~L~NG~~l~G~I~~fD~ftVlL   46 (82)
T 1u1s_A           19 RVPVSIYLVNGIKLQGQIESFDQFVILL   46 (82)
T ss_dssp             TCCEEEEETTSCEEEEEEEEECSSEEEE
T ss_pred             CCcEEEEEeCCcEEEEEEEEEcceEEEE
Confidence            4688888999999999999999998544

>3rux_A BIRA bifunctional protein; biotin-protein ligase, ligase-ligase inhibitor complex; HET: BS5; 1.70A {Mycobacterium tuberculosis} PDB: 3l1a_A 3l2z_A 2cgh_A

Probab=90.42  E-value=0.17  Score=45.80  Aligned_cols=38  Identities=26%  Similarity=0.301  Sum_probs=32.4

Q ss_pred             HhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEe
Q 023166           11 QFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEF   48 (286)
Q Consensus        11 qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~   48 (286)
                      .+++++|+|.+.++++++|+++++|.+-.|+|.+..+.
T Consensus       221 ~~~g~~V~v~~~~~~~~~G~~~gId~~G~L~v~~~~g~  258 (270)
T 3rux_A          221 LTIGSRVRVELPGGQDVVGIARDIDDQGRLCLDVGGRT  258 (270)
T ss_dssp             SSTTSEEEEECTTSCEEEEEEEEECTTSCEEEEETTEE
T ss_pred             cccCCEEEEEECCCeEEEEEEEEECCCCeEEEEECCCE
Confidence            36789999998889999999999999999999755443

>1ib8_A Conserved protein SP14.3; nucleic acid binding protein, ribosomal protein, essential gene, structural genomics; NMR {Streptococcus pneumoniae} SCOP: b.38.2.1 d.52.4.1

Probab=90.37  E-value=0.27  Score=41.79  Aligned_cols=38  Identities=13%  Similarity=0.344  Sum_probs=30.7

Q ss_pred             hhhhHHHHhcCCEEEEEE----eCCcEEEEEEEEeccccceEe
Q 023166            4 SKSSKMLQFINYRMRVTI----QDGRQLVGKFMAFDRHMNLVL   42 (286)
Q Consensus         4 ~k~skL~qlIgkRVRVtL----qDGR~fvGtLlAFDKhMNLVL   42 (286)
                      -+..++.+|+++.|+|+|    .+.+.|+|+|.++|.. +++|
T Consensus        94 ~~~~df~r~~G~~V~V~l~~~~~g~k~~~G~L~~~~~~-~v~l  135 (164)
T 1ib8_A           94 KTKDAVAGAVGKYIHVGLYQAIDKQKVFEGTLLAFEED-ELTM  135 (164)
T ss_dssp             SSHHHHHHHCSEEEEEECSSCSSSCSEEEEEEEEEETT-EEEE
T ss_pred             CCHHHHHHhCCcEEEEEEecccCCceEEEEEEEEEeCC-EEEE
Confidence            355678899999999999    4559999999999865 3444

>2rm4_A CG6311-PB, DM EDC3; enhancer of mRNA decapping, P-BODY component, SM-like protein,, protein binding; NMR {Drosophila melanogaster}

Probab=88.37  E-value=1.4  Score=35.43  Aligned_cols=68  Identities=10%  Similarity=0.150  Sum_probs=51.0

Q ss_pred             HHhcCCEEEEEEeCCc-EEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEeeecC
Q 023166           10 LQFINYRMRVTIQDGR-QLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMTVEG   88 (286)
Q Consensus        10 ~qlIgkRVRVtLqDGR-~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIsVe~   88 (286)
                      .+||++-|.|+..|.- .|.|.++.+|+. +|+|.++...-.               -.+...-.|.+|...|.++.+-+
T Consensus         8 edwiG~~VSI~C~d~LGVyQG~I~~V~~~-~ItL~kaFrNGi---------------plk~~~~EVtLsa~DI~~L~IIe   71 (103)
T 2rm4_A            8 QDWIGCAVSIACDEVLGVFQGLIKQISAE-EITIVRAFRNGV---------------PLRKQNAEVVLKCTDIRSIDLIE   71 (103)
T ss_dssp             GGGTTCEEEEEECTTTCEEEEEEEEEETT-EEEEEEEEETTE---------------ECSCSSSCEEEETTTEEEEEEEE
T ss_pred             cceeceEEEEeeCCcceEeeEEEEEcccc-eeEEhhhhhcCc---------------CcCCCCceEEEEecchhheeeec
Confidence            4899999999998887 999999999964 588888743211               11334456888888899888877


Q ss_pred             CCCCh
Q 023166           89 PPPPE   93 (286)
Q Consensus        89 PPp~d   93 (286)
                      ..-.|
T Consensus        72 ~~~~~   76 (103)
T 2rm4_A           72 PAKQD   76 (103)
T ss_dssp             CCCCC
T ss_pred             ccccc
Confidence            65444

>3hfn_A ASL2047 protein; HFQ, SM, RNA-binding protein, sRNA, translational regulation binding protein; 2.31A {Nostoc SP}

Probab=87.66  E-value=0.94  Score=34.35  Aligned_cols=35  Identities=11%  Similarity=0.295  Sum_probs=28.7

Q ss_pred             hHHHHhcCC--EEEEEEeCCcEEEEEEEEeccccceE
Q 023166            7 SKMLQFINY--RMRVTIQDGRQLVGKFMAFDRHMNLV   41 (286)
Q Consensus         7 skL~qlIgk--RVRVtLqDGR~fvGtLlAFDKhMNLV   41 (286)
                      ..|.+||..  .|+|+|.+|..|+|++.-+|.|+=++
T Consensus        14 R~lQ~~Ik~k~~V~I~L~tGd~l~G~i~WQD~~cl~L   50 (72)
T 3hfn_A           14 RQLQNLIKQAAPVEIKLVTGDAITGRVLWQDPTCVCI   50 (72)
T ss_dssp             HHHHHHHSSCCEEEEEETTSCEEEEEEEEECSSEEEE
T ss_pred             HHHHHHHhhCceEEEEecCCCEEEEEEEEECCCEEEE
Confidence            457788874  67788899999999999999987433

>3pgw_B SM B; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_A

Probab=87.09  E-value=2.6  Score=38.25  Aligned_cols=17  Identities=12%  Similarity=0.192  Sum_probs=13.3

Q ss_pred             hcCCEEEEEEeCCcEEE
Q 023166           12 FINYRMRVTIQDGRQLV   28 (286)
Q Consensus        12 lIgkRVRVtLqDGR~fv   28 (286)
                      -+|+.+.+.|.|-.||+
T Consensus        33 gFDq~MNLVL~Da~E~~   49 (231)
T 3pgw_B           33 AFDKHMNLILCDCDEFR   49 (231)
T ss_pred             EEcccccEEecCEEEEE
Confidence            35778888888888875

>3hfo_A SSR3341 protein; HFQ, SM, RNA-binding protein, sRNA, translational regulation binding protein; 1.30A {Synechocystis SP}

Probab=84.34  E-value=1.4  Score=33.15  Aligned_cols=35  Identities=14%  Similarity=0.157  Sum_probs=28.5

Q ss_pred             hHHHHhcC--CEEEEEEeCCcEEEEEEEEeccccceE
Q 023166            7 SKMLQFIN--YRMRVTIQDGRQLVGKFMAFDRHMNLV   41 (286)
Q Consensus         7 skL~qlIg--kRVRVtLqDGR~fvGtLlAFDKhMNLV   41 (286)
                      ..|.+||-  ..|.|.|.+|..++|.+.-||.|+=++
T Consensus        12 R~lQ~~ik~k~~V~I~L~tG~~l~G~i~WQD~~cl~L   48 (70)
T 3hfo_A           12 RQVQLLIKDQTPVEIKLLTGDSLFGTIRWQDTDGLGL   48 (70)
T ss_dssp             HHHHHHHHHTCEEEEEETTSCEEEEEEEEECSSEEEE
T ss_pred             HHHHHHHhhCceEEEEecCCCEEEEEEEEeCCCEEEE
Confidence            35666775  578888999999999999999997444

>2xk0_A Polycomb protein PCL; transcription, aromatic CAGE; NMR {Drosophila melanogaster}

Probab=84.01  E-value=2.1  Score=32.31  Aligned_cols=39  Identities=18%  Similarity=0.237  Sum_probs=31.5

Q ss_pred             cCCEEEEEEeCCcEEEEEEEEeccccceE-eCceEEeecC
Q 023166           13 INYRMRVTIQDGRQLVGKFMAFDRHMNLV-LGDCEEFRKL   51 (286)
Q Consensus        13 IgkRVRVtLqDGR~fvGtLlAFDKhMNLV-LsD~eE~r~i   51 (286)
                      ++..|.|+-+||+.|.||++..+++-=|| .+|-.|++..
T Consensus        18 ~geDVL~rw~DG~fYLGtIVd~~~~~ClV~FeD~S~~Wv~   57 (69)
T 2xk0_A           18 LQEDVFIKCNDGRFYLGTIIDQTSDQYLIRFDDQSEQWCE   57 (69)
T ss_dssp             TTCEEEEECTTSCEEEEEEEEECSSCEEEEETTCCEEEEC
T ss_pred             cCCeEEEEecCCCEEEEEEEecCCceEEEEecCCcceeee
Confidence            67899999999999999998877665444 4788888764

>1bia_A BIRA bifunctional protein; transcription regulation; 2.30A {Escherichia coli} SCOP: a.4.5.1 b.34.1.1 d.104.1.2 PDB: 1bib_A* 1hxd_A* 2ewn_A*

Probab=83.90  E-value=1.2  Score=40.79  Aligned_cols=35  Identities=23%  Similarity=0.360  Sum_probs=29.3

Q ss_pred             HHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCce
Q 023166           10 LQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDC   45 (286)
Q Consensus        10 ~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~   45 (286)
                      ..+++++|+|... +.+++|+++++|.+-.|+|.+.
T Consensus       269 ~~~~g~~V~v~~~-~~~~~G~~~gid~~G~L~v~~~  303 (321)
T 1bia_A          269 DNFINRPVKLIIG-DKEIFGISRGIDKQGALLLEQD  303 (321)
T ss_dssp             BTTTTSEEEEEET-TEEEEEEEEEECTTSCEEEEET
T ss_pred             hhhcCCEEEEEEC-CcEEEEEEEEECCCCeEEEEEC
Confidence            3468999999864 5689999999999999998654

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	286
d1d3bb_	81	b.38.1.1 (B:) B core SNRNP protein {Human (Homo sa	1e-33
d2fwka1	92	b.38.1.1 (A:24-115) U6 snRNA-associated sm-like pr	7e-23
d1b34b_	93	b.38.1.1 (B:) D2 core SNRNP protein {Human (Homo s	5e-21
d1i8fa_	71	b.38.1.1 (A:) Archaeal homoheptameric Sm protein {	1e-17
d1th7a1	76	b.38.1.1 (A:3-78) Archaeal homoheptameric Sm prote	3e-17
d1mgqa_	74	b.38.1.1 (A:) Archaeal homoheptameric Sm protein {	2e-16
d1h641_	71	b.38.1.1 (1:) Archaeal homoheptameric Sm protein {	5e-16
d1ljoa_	75	b.38.1.1 (A:) Archaeal homoheptameric Sm protein {	1e-15
d1n9ra_	68	b.38.1.1 (A:) Small nuclear ribonucleoprotein F, S	5e-14
d1i4k1_	72	b.38.1.1 (1:) Archaeal homoheptameric Sm protein {	6e-14
d1m5q1_	127	b.38.1.1 (1:) Sm-Like archaeal protein Smap3 {Arch	5e-09
d1d3ba_	72	b.38.1.1 (A:) D3 core SNRNP protein {Human (Homo s	1e-06

>d1d3bb_ b.38.1.1 (B:) B core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]} Length = 81

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: B core SNRNP protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  115 bits (290), Expect = 1e-33
 Identities = 55/85 (64%), Positives = 67/85 (78%), Gaps = 4/85 (4%)

Query: 7  SKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEERE 66
          SKMLQ I+YRMR  +QDGR  +G F AFD+HMNL+L DC+EFRK+ P    KN+   ERE
Sbjct: 1  SKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKP----KNSKQAERE 56

Query: 67 DRRTLGLVLLRGEEVISMTVEGPPP 91
          ++R LGLVLLRGE ++SMTVEGPPP
Sbjct: 57 EKRVLGLVLLRGENLVSMTVEGPPP 81

>d2fwka1 b.38.1.1 (A:24-115) U6 snRNA-associated sm-like protein LSM5 {Cryptosporidium parvum [TaxId: 5807]} Length = 92

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: U6 snRNA-associated sm-like protein LSM5
species: Cryptosporidium parvum [TaxId: 5807]

 Score = 88.0 bits (218), Expect = 7e-23
 Identities = 19/91 (20%), Positives = 39/91 (42%), Gaps = 2/91 (2%)

Query: 2  SMSKSSKML-QFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNN 60
          ++     ++ + I  R+ V ++  ++  G    FD ++N+VL D +E+      +     
Sbjct: 2  NIILPLALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGG 61

Query: 61 TNE-EREDRRTLGLVLLRGEEVISMTVEGPP 90
            + +R     L  +LL G  V  +   G P
Sbjct: 62 NKKLKRVMVNRLETILLSGNNVAMLVPGGDP 92

>d1b34b_ b.38.1.1 (B:) D2 core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: D2 core SNRNP protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 83.0 bits (205), Expect = 5e-21
 Identities = 23/77 (29%), Positives = 40/77 (51%), Gaps = 2/77 (2%)

Query: 14 NYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGL 73
          N ++ +  ++ ++L+G+  AFDRH N+VL + +E     P  GK    ++     R +  
Sbjct: 14 NTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKGKKKSKPVNKDRYISK 73

Query: 74 VLLRGEEVISMTVEGPP 90
          + LRG+ VI   V   P
Sbjct: 74 MFLRGDSVI--VVLRNP 88

>d1i8fa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Pyrobaculum aerophilum [TaxId: 13773]} Length = 71

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Archaeal homoheptameric Sm protein
species: Archaeon Pyrobaculum aerophilum [TaxId: 13773]

 Score = 73.2 bits (180), Expect = 1e-17
 Identities = 20/86 (23%), Positives = 38/86 (44%), Gaps = 18/86 (20%)

Query: 6  SSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEER 65
           + +   I  ++ V ++D  ++ G   +FD+H+NL+L D EE                  
Sbjct: 4  GATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIID--------------- 48

Query: 66 EDRRTLGLVLLRGEEVISMTVEGPPP 91
           +    G +++RGE V+ +    P P
Sbjct: 49 GNVYKRGTMVVRGENVLFI---SPVP 71

>d1th7a1 b.38.1.1 (A:3-78) Archaeal homoheptameric Sm protein {Sulfolobus solfataricus [TaxId: 2287]} Length = 76

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Archaeal homoheptameric Sm protein
species: Sulfolobus solfataricus [TaxId: 2287]

 Score = 72.4 bits (178), Expect = 3e-17
 Identities = 22/88 (25%), Positives = 46/88 (52%), Gaps = 17/88 (19%)

Query: 1  MS-MSK-SSKMLQ-FINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGK 57
          M+ +++ + K+L   +N  + V ++  +++ G   ++D+HMNLVL D EE +        
Sbjct: 1  MNFLAETAHKVLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQS------- 53

Query: 58 KNNTNEEREDRRTLGLVLLRGEEVISMT 85
                     + LG +++RG+ VI ++
Sbjct: 54 -------DGSGKKLGTIVIRGDNVILIS 74

>d1mgqa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]} Length = 74

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Archaeal homoheptameric Sm protein
species: Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]

 Score = 70.1 bits (172), Expect = 2e-16
 Identities = 23/86 (26%), Positives = 40/86 (46%), Gaps = 15/86 (17%)

Query: 1  MSMSKSSKMLQ-FINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKN 59
          +++ +    L   +N  + + ++  R+  G   +FD HMNLVL D EE            
Sbjct: 2  VNVQRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELED--------- 52

Query: 60 NTNEEREDRRTLGLVLLRGEEVISMT 85
                E  R LG VL+RG+ ++ ++
Sbjct: 53 -----GEVTRRLGTVLIRGDNIVYIS 73

>d1h641_ b.38.1.1 (1:) Archaeal homoheptameric Sm protein {Archaeon Pyrococcus abyssi [TaxId: 29292]} Length = 71

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Archaeal homoheptameric Sm protein
species: Archaeon Pyrococcus abyssi [TaxId: 29292]

 Score = 69.0 bits (169), Expect = 5e-16
 Identities = 15/75 (20%), Positives = 37/75 (49%), Gaps = 14/75 (18%)

Query: 11 QFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRT 70
          + ++  + V ++ G +  G+ + +D H+N+VL D E  +                E  + 
Sbjct: 9  RSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQD--------------GEVVKR 54

Query: 71 LGLVLLRGEEVISMT 85
           G +++RG+ V++++
Sbjct: 55 YGKIVIRGDNVLAIS 69

>d1ljoa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Archaeoglobus fulgidus, AF-Sm2 [TaxId: 2234]} Length = 75

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Archaeal homoheptameric Sm protein
species: Archaeon Archaeoglobus fulgidus, AF-Sm2 [TaxId: 2234]

 Score = 67.8 bits (166), Expect = 1e-15
 Identities = 23/88 (26%), Positives = 42/88 (47%), Gaps = 16/88 (18%)

Query: 2  SMSKSSKMLQ-FINYRMRVTIQ-DGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKN 59
          +M   ++M++  +   +RV ++ +  QLVGK    D +MNL L +  E +          
Sbjct: 2  AMVLPNQMVKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECKG--------- 52

Query: 60 NTNEEREDRRTLGLVLLRGEEVISMTVE 87
                E  R+LG ++LRG  V+ +  +
Sbjct: 53 -----EEKVRSLGEIVLRGNNVVLIQPQ 75

>d1n9ra_ b.38.1.1 (A:) Small nuclear ribonucleoprotein F, Smf {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 68

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Small nuclear ribonucleoprotein F, Smf
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 63.6 bits (155), Expect = 5e-14
 Identities = 17/82 (20%), Positives = 31/82 (37%), Gaps = 18/82 (21%)

Query: 11 QFINYRMRVTIQD-GRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRR 69
            +N+R+ V ++    +  G  ++ D + NL L + EEF                     
Sbjct: 3  GLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEF--------------VAGVSHG 48

Query: 70 TLGLVLLRGEEVISMTVEGPPP 91
          TLG + +R   V+ +      P
Sbjct: 49 TLGEIFIRCNNVLYI---RELP 67

>d1i4k1_ b.38.1.1 (1:) Archaeal homoheptameric Sm protein {Archaeon Archaeoglobus fulgidus, AF-Sm1 [TaxId: 2234]} Length = 72

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Archaeal homoheptameric Sm protein
species: Archaeon Archaeoglobus fulgidus, AF-Sm1 [TaxId: 2234]

 Score = 63.2 bits (154), Expect = 6e-14
 Identities = 21/75 (28%), Positives = 36/75 (48%), Gaps = 14/75 (18%)

Query: 11 QFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRT 70
          + +   + V ++ GR+  G    +D HMNLVL D EE +                E  R 
Sbjct: 10 RSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQN--------------GEVVRK 55

Query: 71 LGLVLLRGEEVISMT 85
          +G V++RG+ V+ ++
Sbjct: 56 VGSVVIRGDTVVFVS 70

>d1m5q1_ b.38.1.1 (1:) Sm-Like archaeal protein Smap3 {Archaeon Pyrobaculum aerophilum [TaxId: 13773]} Length = 127

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Sm-Like archaeal protein Smap3
species: Archaeon Pyrobaculum aerophilum [TaxId: 13773]

 Score = 51.3 bits (123), Expect = 5e-09
 Identities = 24/129 (18%), Positives = 38/129 (29%), Gaps = 41/129 (31%)

Query: 11  QFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRT 70
             +   ++V + +G    G   A D  +N+VL +                   E+ +R  
Sbjct: 7   NLLGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASN-------------KAGEKFNR-- 51

Query: 71  LGLVLLRG---------EEVISMT-----VEGPPP-----PEESRAK----AVSASAVAG 107
              V +           E  I M       E   P      EE+        V  S +  
Sbjct: 52  ---VFIMYRYIVHIDSTERRIDMREFAKQAEKIFPGMVKYIEETNVVLIGDKVRVSEIGV 108

Query: 108 PGIGRAAGR 116
            G+G  A R
Sbjct: 109 EGVGPVAER 117

>d1d3ba_ b.38.1.1 (A:) D3 core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]} Length = 72

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: D3 core SNRNP protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.2 bits (102), Expect = 1e-06
 Identities = 12/81 (14%), Positives = 27/81 (33%), Gaps = 15/81 (18%)

Query: 7  SKMLQ-FINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEER 65
           K+L     + +      G    GK +  + +MN  + +     +     G+        
Sbjct: 4  IKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYR----DGRV------- 52

Query: 66 EDRRTLGLVLLRGEEVISMTV 86
               L  V +RG ++  + +
Sbjct: 53 ---AQLEQVYIRGCKIRFLIL 70

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	286
d1d3bb_	81	B core SNRNP protein {Human (Homo sapiens) [TaxId:	99.95
d2fwka1	92	U6 snRNA-associated sm-like protein LSM5 {Cryptosp	99.88
d1b34b_	93	D2 core SNRNP protein {Human (Homo sapiens) [TaxId	99.87
d1i8fa_	71	Archaeal homoheptameric Sm protein {Archaeon Pyrob	99.85
d1i4k1_	72	Archaeal homoheptameric Sm protein {Archaeon Archa	99.84
d1th7a1	76	Archaeal homoheptameric Sm protein {Sulfolobus sol	99.84
d1h641_	71	Archaeal homoheptameric Sm protein {Archaeon Pyroc	99.83
d1mgqa_	74	Archaeal homoheptameric Sm protein {Archaeon Metha	99.82
d1ljoa_	75	Archaeal homoheptameric Sm protein {Archaeon Archa	99.8
d1n9ra_	68	Small nuclear ribonucleoprotein F, Smf {Baker's ye	99.78
d1d3ba_	72	D3 core SNRNP protein {Human (Homo sapiens) [TaxId	99.74
d1b34a_	80	D1 core SNRNP protein {Human (Homo sapiens) [TaxId	99.63
d1m5q1_	127	Sm-Like archaeal protein Smap3 {Archaeon Pyrobacul	99.54
d2vxfa1	80	LSM14 homolog A (Lsm14a) {Zebrafish (Danio rerio)	97.38
d1biaa2	47	Biotin repressor/biotin holoenzyme synthetase, C-t	96.57
d1ycya1	66	Hypothetical protein PF1955 {Pyrococcus furiosus [	94.3
d1ib8a1	74	Hypothetical protein SP14.3 (SP0552) {Streptococcu	93.97
d1kq1a_	60	Pleiotropic translational regulator Hfq {Staphyloc	90.75
d1u1sa1	66	Pleiotropic translational regulator Hfq {Pseudomon	87.11
d1sg5a1	86	Inhibitor of Rho Rof {Escherichia coli [TaxId: 562	83.27

>d1d3bb_ b.38.1.1 (B:) B core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: B core SNRNP protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.95  E-value=2.3e-28  Score=186.53  Aligned_cols=81  Identities=67%  Similarity=1.177  Sum_probs=72.0

Q ss_pred             hHHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEeee
Q 023166            7 SKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMTV   86 (286)
Q Consensus         7 skL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIsV   86 (286)
                      +||.+|||+||+|+|+|||+|+|+|+|||+||||||+||+|++....++.+    ..+.+++|.||++||||+||++|++
T Consensus         1 s~L~~~l~~rv~V~l~dgR~~~G~L~~~D~~~NlvL~~~~E~~~~~~~~~~----~~~~~~~r~lG~v~IRG~~Iv~i~~   76 (81)
T d1d3bb_           1 SKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSK----QAEREEKRVLGLVLLRGENLVSMTV   76 (81)
T ss_dssp             CCCGGGTTSEEEEEETTCCEEEEEEEECCTTCCEEEEEEEEEEEECCSSTT----SCCEEEEEEEEEEEECGGGEEEEEE
T ss_pred             ChhHHHCCCEEEEEEcCCCEEEEEEEEECCccCEEEcCEEEEEeecCcccc----ccccceEEEeeeEEEeCCEEEEEEc
Confidence            479999999999999999999999999999999999999999876554332    2346678999999999999999999


Q ss_pred             cCCCC
Q 023166           87 EGPPP   91 (286)
Q Consensus        87 e~PPp   91 (286)
                      +++||
T Consensus        77 ~~~pp   81 (81)
T d1d3bb_          77 EGPPP   81 (81)
T ss_dssp             EECCC
T ss_pred             cCCCC
Confidence            99876

>d2fwka1 b.38.1.1 (A:24-115) U6 snRNA-associated sm-like protein LSM5 {Cryptosporidium parvum [TaxId: 5807]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: U6 snRNA-associated sm-like protein LSM5
species: Cryptosporidium parvum [TaxId: 5807]

Probab=99.88  E-value=1.5e-23  Score=162.69  Aligned_cols=84  Identities=23%  Similarity=0.344  Sum_probs=64.0

Q ss_pred             hhHHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCC-CCcccccceeEeceEEecCceeEEe
Q 023166            6 SSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKN-NTNEEREDRRTLGLVLLRGEEVISM   84 (286)
Q Consensus         6 ~skL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~-~~~~e~eekR~LGlVLIRGenIVSI   84 (286)
                      -+.|.+|++++|+|+|+|||+|+|+|+|||+||||||+||+|++....++.... ......+.+|+||++|||||||++|
T Consensus         7 l~~L~~~l~k~V~V~l~~gr~~~G~L~~~D~~~NlvL~d~~E~~~~~~~~~~~~~~~~~~~~~~r~lg~~~iRG~~Vv~I   86 (92)
T d2fwka1           7 LALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGGNKKLKRVMVNRLETILLSGNNVAML   86 (92)
T ss_dssp             HHHHHHTBTSBCEEEETTTEEECCEEEEECTTCCEEEESCCEEEC---------------CEECCCCSEEEECGGGEEEE
T ss_pred             HHHHHHHcCCEEEEEEcCCCEEEEEEEEEcCCCCEEEeeEEEEEecCCccccccccccccccceeEcceEEEeCCEEEEE
Confidence            346889999999999999999999999999999999999999987655432211 1122456789999999999999999


Q ss_pred             eecCC
Q 023166           85 TVEGP   89 (286)
Q Consensus        85 sVe~P   89 (286)
                      +-.+.
T Consensus        87 ~p~~~   91 (92)
T d2fwka1          87 VPGGD   91 (92)
T ss_dssp             ESSSC
T ss_pred             EeCCC
Confidence            86543

>d1b34b_ b.38.1.1 (B:) D2 core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: D2 core SNRNP protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.87  E-value=7.2e-23  Score=160.20  Aligned_cols=81  Identities=28%  Similarity=0.502  Sum_probs=57.0

Q ss_pred             hHHHHhc--CCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEe
Q 023166            7 SKMLQFI--NYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISM   84 (286)
Q Consensus         7 skL~qlI--gkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSI   84 (286)
                      +.|.+++  ++||+|+|+|+|+|+|+|+|||+||||||+||+|++....++.+.........++|+||++|||||||++|
T Consensus         5 ~~l~~~~~~~~rV~V~lr~~r~~~G~L~afD~~~NlVL~d~~E~~~~~~~~~~~~~~~~~~~~~R~lg~~liRGdnVv~I   84 (93)
T d1b34b_           5 SVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKGKKKSKPVNKDRYISKMFLRGDSVIVV   84 (93)
T ss_dssp             HHHHHHHHHTCEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEC-------------------CEEEEEEEECGGGEEEE
T ss_pred             HHHHHHHhCCcEEEEEECCCCEEEEEEEEeccceeEEeeceEEEEEecCCccccccccccceeEEEeceEEEeCCEEEEE
Confidence            4466676  89999999999999999999999999999999999986554332211122345789999999999999998


Q ss_pred             eec
Q 023166           85 TVE   87 (286)
Q Consensus        85 sVe   87 (286)
                      ...
T Consensus        85 ~~~   87 (93)
T d1b34b_          85 LRN   87 (93)
T ss_dssp             EEC
T ss_pred             EcC
Confidence            654

>d1i8fa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Pyrobaculum aerophilum [TaxId: 13773]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Archaeal homoheptameric Sm protein
species: Archaeon Pyrobaculum aerophilum [TaxId: 13773]

Probab=99.85  E-value=6.8e-22  Score=147.48  Aligned_cols=65  Identities=28%  Similarity=0.515  Sum_probs=60.3

Q ss_pred             hhHHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEee
Q 023166            6 SSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMT   85 (286)
Q Consensus         6 ~skL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIs   85 (286)
                      .+.|.+++|++|+|+|+|||+|+|+|++||+||||+|+||+|++.               ++++.+|++||||+||++|+
T Consensus         4 ~~~L~~~~~k~V~V~Lk~g~~~~G~L~~~D~~mNivL~~~~e~~~---------------~~~~~~g~v~iRG~~I~~I~   68 (71)
T d1i8fa_           4 GATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIID---------------GNVYKRGTMVVRGENVLFIS   68 (71)
T ss_dssp             HHHHHTTTTSEEEEEEGGGEEEEEEEEEECTTCCEEEEEEEEEET---------------TEEEEEEEEEECGGGEEEEE
T ss_pred             hHHHHHhCCCEEEEEECCCCEEEEEEEEECCCcceEEccEEEEEC---------------CCEEEcceEEEeCCeEEEEe
Confidence            578999999999999999999999999999999999999999853               24688999999999999996

>d1i4k1_ b.38.1.1 (1:) Archaeal homoheptameric Sm protein {Archaeon Archaeoglobus fulgidus, AF-Sm1 [TaxId: 2234]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Archaeal homoheptameric Sm protein
species: Archaeon Archaeoglobus fulgidus, AF-Sm1 [TaxId: 2234]

Probab=99.84  E-value=2.8e-21  Score=143.84  Aligned_cols=65  Identities=32%  Similarity=0.543  Sum_probs=59.2

Q ss_pred             hHHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEee
Q 023166            7 SKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMT   85 (286)
Q Consensus         7 skL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIs   85 (286)
                      ..|.+++|++|+|+|+|||+|+|+|++||+||||+|+||+|+..              .++++.+|+++|||+||++|+
T Consensus         6 ~~L~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~~~~e~~~--------------~~~~~~~g~~~IRG~~I~~Is   70 (72)
T d1i4k1_           6 DVLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQN--------------GEVVRKVGSVVIRGDTVVFVS   70 (72)
T ss_dssp             HHHHTTTTSEEEEEEGGGCEEEEEEEEECTTCCEEEEEEEEESS--------------SSEEEEEEEEEECGGGEEEEE
T ss_pred             HHHHHhCCCEEEEEECCCCEEEEEEEEEcCCCCeEEeeEEEEec--------------CCeEeEcceEEEeCCeEEEEE
Confidence            45789999999999999999999999999999999999999853              246789999999999999996

>d1th7a1 b.38.1.1 (A:3-78) Archaeal homoheptameric Sm protein {Sulfolobus solfataricus [TaxId: 2287]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Archaeal homoheptameric Sm protein
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=99.84  E-value=4.1e-21  Score=144.44  Aligned_cols=71  Identities=27%  Similarity=0.530  Sum_probs=62.3

Q ss_pred             CchhhhHHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCcee
Q 023166            2 SMSKSSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEV   81 (286)
Q Consensus         2 ~~~k~skL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenI   81 (286)
                      +......|.+++|++|+|+|+||++|+|+|.+||+||||+|+||+|+..              ..+++.+|++||||+||
T Consensus         5 ~~~~~~~L~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~~~~e~~~--------------~~~~~~~~~v~iRG~~I   70 (76)
T d1th7a1           5 AETAHKVLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQS--------------DGSGKKLGTIVIRGDNV   70 (76)
T ss_dssp             CHHHHHHHHHHTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEECS--------------SSCEEEEEEEEECGGGE
T ss_pred             cccHHHHHHHhCCCEEEEEECCCCEEEEEEEEECCCCCEEEeEEEEEec--------------CCcccCcceEEEECCEE
Confidence            3344566889999999999999999999999999999999999999753              24578999999999999


Q ss_pred             EEeee
Q 023166           82 ISMTV   86 (286)
Q Consensus        82 VSIsV   86 (286)
                      ++|+.
T Consensus        71 ~~I~~   75 (76)
T d1th7a1          71 ILISP   75 (76)
T ss_dssp             EEEEE
T ss_pred             EEEEe
Confidence            99974

>d1h641_ b.38.1.1 (1:) Archaeal homoheptameric Sm protein {Archaeon Pyrococcus abyssi [TaxId: 29292]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Archaeal homoheptameric Sm protein
species: Archaeon Pyrococcus abyssi [TaxId: 29292]

Probab=99.83  E-value=5.3e-21  Score=141.64  Aligned_cols=64  Identities=23%  Similarity=0.546  Sum_probs=58.6

Q ss_pred             HHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEee
Q 023166            8 KMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMT   85 (286)
Q Consensus         8 kL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIs   85 (286)
                      -|.++++++|+|+|+||++|+|+|++||+||||+|+||+|+..              .++++.+|++||||+||++|+
T Consensus         6 ~L~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~~~~e~~~--------------~~~~~~l~~~~IRG~~I~~Is   69 (71)
T d1h641_           6 VIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQD--------------GEVVKRYGKIVIRGDNVLAIS   69 (71)
T ss_dssp             HHHTTTTSEEEEEETTSEEEEEEEEEECTTCCEEEEEEEEEET--------------TEEEEEEEEEEECGGGEEEEE
T ss_pred             HHHHhCCCEEEEEEcCCCEEEEEEEEECCCCCeEEeeEEEEec--------------CCcEeEcCcEEEECCeEEEEe
Confidence            4779999999999999999999999999999999999999863              235789999999999999996

>d1mgqa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Archaeal homoheptameric Sm protein
species: Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]

Probab=99.82  E-value=1.4e-20  Score=140.65  Aligned_cols=65  Identities=34%  Similarity=0.603  Sum_probs=59.0

Q ss_pred             hHHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEee
Q 023166            7 SKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMT   85 (286)
Q Consensus         7 skL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIs   85 (286)
                      +.|.+++|++|+|+|+||++|+|+|++||+||||+|+||+|++.              .++++.+|++||||+||++|+
T Consensus         9 ~~L~~~~~k~V~V~lk~g~~~~G~L~~~D~~mNl~L~~~~e~~~--------------~~~~~~~~~~~IRG~~I~~I~   73 (74)
T d1mgqa_           9 DALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELED--------------GEVTRRLGTVLIRGDNIVYIS   73 (74)
T ss_dssp             HHHHHTTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEEET--------------TEEEEEEEEEEECGGGEEEEE
T ss_pred             HHHHHhCCCeEEEEECCCCEEEEEEEEECCCCCeEEeeEEEEeC--------------CCeEeEcceEEEeCCEEEEEe
Confidence            45779999999999999999999999999999999999999863              245789999999999999985

>d1ljoa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Archaeoglobus fulgidus, AF-Sm2 [TaxId: 2234]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Archaeal homoheptameric Sm protein
species: Archaeon Archaeoglobus fulgidus, AF-Sm2 [TaxId: 2234]

Probab=99.80  E-value=5.6e-20  Score=138.42  Aligned_cols=67  Identities=31%  Similarity=0.495  Sum_probs=59.1

Q ss_pred             hhHHHHhcCCEEEEEEeC-CcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEe
Q 023166            6 SSKMLQFINYRMRVTIQD-GRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISM   84 (286)
Q Consensus         6 ~skL~qlIgkRVRVtLqD-GR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSI   84 (286)
                      ...|.+|++++|+|+|++ +|+|+|+|++||+||||+|+||+|+..              ..+++.+|++||||+||++|
T Consensus         7 ~~~L~~~~~~~V~V~lk~~~~~~~G~L~~~D~~mNlvL~~~~e~~~--------------~~~~~~~g~~~IRG~~I~~I   72 (75)
T d1ljoa_           7 NQMVKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECKG--------------EEKVRSLGEIVLRGNNVVLI   72 (75)
T ss_dssp             HHHHHHTTTSEEEEEETTCSSEEEEEEEEECTTCCEEEEEEEEEET--------------TEEEEEEEEEEECGGGEEEE
T ss_pred             HHHHHHhcCCEEEEEEECCCEEEEEEEEEEcCCCcEEEeEEEEEcC--------------CCcEeEcceEEEeCCEEEEE
Confidence            346788999999999985 589999999999999999999999753              24578999999999999999


Q ss_pred             ee
Q 023166           85 TV   86 (286)
Q Consensus        85 sV   86 (286)
                      +.
T Consensus        73 ~p   74 (75)
T d1ljoa_          73 QP   74 (75)
T ss_dssp             EE
T ss_pred             EC
Confidence            74

>d1n9ra_ b.38.1.1 (A:) Small nuclear ribonucleoprotein F, Smf {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Small nuclear ribonucleoprotein F, Smf
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.78  E-value=1.2e-19  Score=134.36  Aligned_cols=63  Identities=25%  Similarity=0.463  Sum_probs=56.3

Q ss_pred             HHHhcCCEEEEEEe-CCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEee
Q 023166            9 MLQFINYRMRVTIQ-DGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMT   85 (286)
Q Consensus         9 L~qlIgkRVRVtLq-DGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIs   85 (286)
                      |.+++|++|.|+|+ ++++|+|+|++||+||||+|+||+|+..              .+.++.||+++|||+||++|.
T Consensus         1 L~~~~~~~V~V~Lk~~~~~~~G~L~~~D~~mNlvL~~~~e~~~--------------~~~~~~lg~~~IRG~nI~~I~   64 (68)
T d1n9ra_           1 LKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVA--------------GVSHGTLGEIFIRCNNVLYIR   64 (68)
T ss_dssp             CGGGTTSEEEEEESSTTEEEEEEEEECCTTTCEEEEEEEEEET--------------TEEEEECCSEEECGGGEEEEE
T ss_pred             ChhHCCCEEEEEEEcCCEEEEEEEEEECCcCceEEeeEEEEec--------------CCcccCcCeEEEECCEEEEEE
Confidence            57899999999999 5688999999999999999999999753              235678999999999999996

>d1d3ba_ b.38.1.1 (A:) D3 core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: D3 core SNRNP protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.74  E-value=4.1e-18  Score=126.84  Aligned_cols=66  Identities=14%  Similarity=0.169  Sum_probs=59.0

Q ss_pred             HHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEeeec
Q 023166            8 KMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMTVE   87 (286)
Q Consensus         8 kL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIsVe   87 (286)
                      -|.++++++|+|+|+||++|+|+|.+||.||||+|+||+|+..              ..+.+.++.+||||++|.+|++.
T Consensus         6 ~L~~~~g~~V~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~~--------------~~~~~~~~~v~IRG~~I~~i~lp   71 (72)
T d1d3ba_           6 VLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYR--------------DGRVAQLEQVYIRGCKIRFLILP   71 (72)
T ss_dssp             HHHHTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEECT--------------TSCEEEEEEEEECGGGEEEEEEC
T ss_pred             HHHhcCCCEEEEEECCCeEEEEEEEEEcCCeeEEEEEEEEEcC--------------CCcEeEcCeEEEECCEEEEEEcC
Confidence            3678999999999999999999999999999999999998753              12457899999999999999875

>d1b34a_ b.38.1.1 (A:) D1 core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: D1 core SNRNP protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.63  E-value=3.5e-16  Score=118.73  Aligned_cols=67  Identities=16%  Similarity=0.285  Sum_probs=59.7

Q ss_pred             HHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEeeec
Q 023166            8 KMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMTVE   87 (286)
Q Consensus         8 kL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIsVe   87 (286)
                      .|.+++|++|.|+|+||++|+|+|.++|.||||+|+||+|+..              ..+...++.++|||++|.+|++.
T Consensus         5 fL~~~~g~~V~VeLkng~~~~G~L~~~D~~MNl~L~~~~~~~~--------------~~~~~~~~~v~IRG~~Ir~i~lP   70 (80)
T d1b34a_           5 FLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLK--------------NREPVQLETLSIRGNNIRYFILP   70 (80)
T ss_dssp             HHHTCTTCEEEEEETTCCEEEEEEEEECTTCCEEEEEEEEECT--------------TSCCEEEEEEEECGGGEEEEECC
T ss_pred             HHHHcCCCEEEEEECCCCEEEEEEEEEcCCcEEEEEEEEEEcC--------------CCCEEEcccEEEcCCEEEEEECC
Confidence            4678999999999999999999999999999999999998753              12456899999999999999986


Q ss_pred             C
Q 023166           88 G   88 (286)
Q Consensus        88 ~   88 (286)
                      +
T Consensus        71 d   71 (80)
T d1b34a_          71 D   71 (80)
T ss_dssp             T
T ss_pred             C
Confidence            4

>d1m5q1_ b.38.1.1 (1:) Sm-Like archaeal protein Smap3 {Archaeon Pyrobaculum aerophilum [TaxId: 13773]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Sm-Like archaeal protein Smap3
species: Archaeon Pyrobaculum aerophilum [TaxId: 13773]

Probab=99.54  E-value=6.8e-15  Score=120.98  Aligned_cols=66  Identities=14%  Similarity=0.295  Sum_probs=58.5

Q ss_pred             hHHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEeee
Q 023166            7 SKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMTV   86 (286)
Q Consensus         7 skL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIsV   86 (286)
                      +.|.+++|++|.|+|+||++|+|+|.+||.||||+|+||+|...                  ..++.++|||++|++|.+
T Consensus         3 ~~L~~~~gk~V~VeLkng~~~~G~L~~~D~~mNivL~da~~~~~------------------~k~~~v~IRG~~I~~I~~   64 (127)
T d1m5q1_           3 AELNNLLGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASNKAG------------------EKFNRVFIMYRYIVHIDS   64 (127)
T ss_dssp             HHHHTTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEETTC------------------CEEEEEEECGGGEEEEEE
T ss_pred             hHHHHhCCCEEEEEECCCCEEEEEEEEECCCceEEEeEEEECCC------------------CcccEEEEeCCeEEEEEc
Confidence            57999999999999999999999999999999999999987421                  136789999999999998


Q ss_pred             cCCC
Q 023166           87 EGPP   90 (286)
Q Consensus        87 e~PP   90 (286)
                      .+..
T Consensus        65 ~e~~   68 (127)
T d1m5q1_          65 TERR   68 (127)
T ss_dssp             CSCC
T ss_pred             chhh
Confidence            8754

>d2vxfa1 b.38.1.5 (A:6-85) LSM14 homolog A (Lsm14a) {Zebrafish (Danio rerio) [TaxId: 7955]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: LSM14 N-terminal domain-like
domain: LSM14 homolog A (Lsm14a)
species: Zebrafish (Danio rerio) [TaxId: 7955]

Probab=97.38  E-value=0.00049  Score=51.64  Aligned_cols=75  Identities=16%  Similarity=0.340  Sum_probs=59.3

Q ss_pred             hcCCEEEEEEeCCcEEEEEEEEeccc-cceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEeeecCCC
Q 023166           12 FINYRMRVTIQDGRQLVGKFMAFDRH-MNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMTVEGPP   90 (286)
Q Consensus        12 lIgkRVRVtLqDGR~fvGtLlAFDKh-MNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIsVe~PP   90 (286)
                      ||+++|.+..+.+-.|+|+|..+|.+ .-|.|.||.-|-+..++...     +.--....+..|+.||+.|..++|.++|
T Consensus         2 yIGs~IsLISk~dIRYeGiL~~Id~~~sTi~L~nVrsfGTEgR~~~~-----~ipp~~~vy~~IvFrgsDIKdL~v~e~p   76 (80)
T d2vxfa1           2 YIGSKISLISKAEIRYEGILYTIDTENSTVALAKVRSFGTEDRPTDR-----PIAPRDETFEYIIFRGSDIKDLTVCEPP   76 (80)
T ss_dssp             STTSEEEEEETTSCEEEEEEEEEETTTTEEEEEEEEECCSTTSCCSS-----CCCCCCCCEEEEEEETTTEEEEEESSCC
T ss_pred             ccCCEEEEEEcCCcEEEEEEEeeccccCEEEeeeeeEeecCCCCCCC-----ccCCCCcceeEEEEcCcCcceEEeccCC
Confidence            79999999999999999999999966 45899999988765432211     1223345678999999999999998765


Q ss_pred             C
Q 023166           91 P   91 (286)
Q Consensus        91 p   91 (286)
                      .
T Consensus        77 ~   77 (80)
T d2vxfa1          77 K   77 (80)
T ss_dssp             C
T ss_pred             C
Confidence            3

>d1biaa2 b.34.1.1 (A:271-317) Biotin repressor/biotin holoenzyme synthetase, C-terminal domain {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: SH3-like barrel
superfamily: C-terminal domain of transcriptional repressors
family: Biotin repressor (BirA)
domain: Biotin repressor/biotin holoenzyme synthetase, C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=96.57  E-value=0.002  Score=43.12  Aligned_cols=35  Identities=23%  Similarity=0.369  Sum_probs=30.1

Q ss_pred             hcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEE
Q 023166           12 FINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEE   47 (286)
Q Consensus        12 lIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE   47 (286)
                      |+++.|+|.. ++++++|+..++|.+-+|+|.....
T Consensus         1 f~gk~V~v~~-g~~~i~G~a~gId~~G~Lll~t~~g   35 (47)
T d1biaa2           1 FINRPVKLII-GDKEIFGISRGIDKQGALLLEQDGI   35 (47)
T ss_dssp             TTTSEEEEEE-TTEEEEEEEEEECTTSCEEEEETTE
T ss_pred             CCCCEEEEEE-CCeEEEEEEeeECCCCcEEEEECCC
Confidence            7999999976 5688999999999999999975443

>d1ycya1 b.38.1.4 (A:5-70) Hypothetical protein PF1955 {Pyrococcus furiosus [TaxId: 2261]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: PF1955-like
domain: Hypothetical protein PF1955
species: Pyrococcus furiosus [TaxId: 2261]

Probab=94.30  E-value=0.023  Score=40.44  Aligned_cols=43  Identities=14%  Similarity=0.345  Sum_probs=34.1

Q ss_pred             hHHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeec
Q 023166            7 SKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRK   50 (286)
Q Consensus         7 skL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~   50 (286)
                      ..|.+|.++||-|.+.....|+|+|.-||... |.|.|+..+.-
T Consensus         5 ktL~~WKg~kvAv~vgsehSFtGiledFDeEv-iLL~dV~D~~G   47 (66)
T d1ycya1           5 KVLKEWKGHKVAVSVGGDHSFTGTLEDFDEEV-ILLKDVVDVIG   47 (66)
T ss_dssp             HHHHHHTTSEEEEEEC----CEEEEEEECSSE-EEEEEEEETTE
T ss_pred             HHHHHhCCcEEEEEecCcceeEEEhhhcCcce-EeehhhHHHhc
Confidence            35889999999999999999999999999884 78899988753

>d1ib8a1 b.38.2.1 (A:91-164) Hypothetical protein SP14.3 (SP0552) {Streptococcus pneumoniae [TaxId: 1313]}

class: All beta proteins
fold: Sm-like fold
superfamily: YhbC-like, C-terminal domain
family: YhbC-like, C-terminal domain
domain: Hypothetical protein SP14.3 (SP0552)
species: Streptococcus pneumoniae [TaxId: 1313]

Probab=93.97  E-value=0.027  Score=39.98  Aligned_cols=38  Identities=13%  Similarity=0.296  Sum_probs=31.2

Q ss_pred             hhhhHHHHhcCCEEEEEEe----CCcEEEEEEEEeccccceEe
Q 023166            4 SKSSKMLQFINYRMRVTIQ----DGRQLVGKFMAFDRHMNLVL   42 (286)
Q Consensus         4 ~k~skL~qlIgkRVRVtLq----DGR~fvGtLlAFDKhMNLVL   42 (286)
                      -+..++.+|+++.|+|+|+    +-|.|+|+|.++|... |+|
T Consensus         4 ~~~~~f~r~~G~~v~v~l~~p~~g~k~f~G~L~~~~~~~-i~l   45 (74)
T d1ib8a1           4 KTKDAVAGAVGKYIHVGLYQAIDKQKVFEGTLLAFEEDE-LTM   45 (74)
T ss_dssp             SSHHHHHHHCSEEEEEECSSCSSSCSEEEEEEEEEETTE-EEE
T ss_pred             CCHHHHHHhCCCEEEEEEecccCCceEEEEEEEeecCCe-EEE
Confidence            3567899999999999983    5689999999999763 444

>d1kq1a_ b.38.1.2 (A:) Pleiotropic translational regulator Hfq {Staphylococcus aureus [TaxId: 1280]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Pleiotropic translational regulator Hfq
domain: Pleiotropic translational regulator Hfq
species: Staphylococcus aureus [TaxId: 1280]

Probab=90.75  E-value=0.16  Score=35.73  Aligned_cols=33  Identities=15%  Similarity=0.218  Sum_probs=26.7

Q ss_pred             CCEEEEEEeCCcEEEEEEEEeccccceEeCceE
Q 023166           14 NYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCE   46 (286)
Q Consensus        14 gkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~e   46 (286)
                      ...|.|-|.+|-.+.|++++||+|.=|+..|..
T Consensus        14 ~~~VtifL~nGvkl~G~I~~fD~ftvlL~~~~~   46 (60)
T d1kq1a_          14 QTEVTVFFLNGFQMKGVIEEYDKYVVSLNSQGK   46 (60)
T ss_dssp             TCEEEEEETTSCEEEEEEEEECSSEEEEEETTE
T ss_pred             CCcEEEEEECCcEEEEEEEEEcceEEEEEeCCc
Confidence            457788889999999999999999866644443

>d1u1sa1 b.38.1.2 (A:6-71) Pleiotropic translational regulator Hfq {Pseudomonas aeruginosa [TaxId: 287]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Pleiotropic translational regulator Hfq
domain: Pleiotropic translational regulator Hfq
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=87.11  E-value=0.43  Score=33.97  Aligned_cols=28  Identities=21%  Similarity=0.459  Sum_probs=23.4

Q ss_pred             CCEEEEEEeCCcEEEEEEEEeccccceE
Q 023166           14 NYRMRVTIQDGRQLVGKFMAFDRHMNLV   41 (286)
Q Consensus        14 gkRVRVtLqDGR~fvGtLlAFDKhMNLV   41 (286)
                      ...|.|-|.+|-.+.|++++||+|.=|+
T Consensus        14 ~~~VtifL~nGvkl~G~I~~fD~ftvLL   41 (66)
T d1u1sa1          14 RVPVSIYLVNGIKLQGQIESFDQFVILL   41 (66)
T ss_dssp             TCCEEEEETTSCEEEEEEEEECSSEEEE
T ss_pred             CCcEEEEEEcCcEEEEEEEEEcceEEEE
Confidence            3567778899999999999999997443

>d1sg5a1 b.137.1.2 (A:1-86) Inhibitor of Rho Rof {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: Rof/RNase P subunit-like
superfamily: Rof/RNase P subunit-like
family: Rof-like
domain: Inhibitor of Rho Rof
species: Escherichia coli [TaxId: 562]

Probab=83.27  E-value=0.47  Score=35.10  Aligned_cols=56  Identities=21%  Similarity=0.236  Sum_probs=37.6

Q ss_pred             HHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEee
Q 023166            8 KMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMT   85 (286)
Q Consensus         8 kL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIs   85 (286)
                      +|.-..++.++|+|+||..+.|+  +.|    +...+-+||..+.                ..-+...||=++|++|+
T Consensus        19 EiaC~~~~~l~l~l~dG~~~~g~--a~D----~~~~~k~E~L~l~----------------~~~~~~~irLD~I~si~   74 (86)
T d1sg5a1          19 ELACQHHLMLTLELKDGEKLQAK--ASD----LVSRKNVEYLVVE----------------AAGETRELRLDKITSFS   74 (86)
T ss_dssp             HHHHTTTTCEEEECTTTCCEEES--SCE----EECCSSSCEEEEE----------------ETTEEEEESTTCCSEEE
T ss_pred             HHHHHcCCcEEEEEeCCCEEEEE--EEE----eEEecCeEEEEEe----------------cCCCeEEEEeceEEeec
Confidence            44556789999999999999984  344    3333445555431                11245778889999885